fix: resolve four frontend/backend issues

- Fix ProjectsPage tests by wrapping renders in MemoryRouter (9 passing)
- Improve session auto-naming to 'project / repo / tool' format
- Add missing /users/me/sessions endpoint for sidebar session loading
- Handle git history 500s: catch RuntimeError in endpoints, graceful empty repo handling
- Add git status badge and discard-changes button to FileEditor toolbar

Quality gates: tsc pass, build pass, Python syntax pass

.atl/.skill-registry.cache.json

@@ -1,3 +0,0 @@
-{
-  "fingerprint": "c36b11ec5edebc02aa51b1113a7a11dc2559e812"
-}

.atl/skill-registry.md

@@ -1,35 +0,0 @@
-# Skill Registry — headquarter
-
-<!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
-
-Last updated: 2026-06-02
-
-## Sources scanned
-
-- .opencode/skills
-- .claude/skills
-- /home/alex/.config/opencode/skills
-
-## Contract
-
-**Delegator use only.** This registry is an index, not a summary. Any agent that launches subagents reads it to select relevant skills, then passes exact `SKILL.md` paths for the subagent to read before work.
-
-`SKILL.md` remains the source of truth. Do not inject generated summaries or compact rules by default; pass paths so subagents load the full runtime contract and preserve author intent.
-
-## Skills
-
-| Skill | Trigger / description | Scope | Path |
-| --- | --- | --- | --- |
-| `auto-commit` | Use when you are making multiple edits or completing significant work in a git repository to automatically create commits | user | `/home/alex/.config/opencode/skills/auto-commit/SKILL.md` |
-| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-apply-change/SKILL.md` |
-| `openspec-archive-change` | Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-archive-change/SKILL.md` |
-| `openspec-explore` | Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-explore/SKILL.md` |
-| `openspec-propose` | Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-propose/SKILL.md` |
-| `sift-backlog` | Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open. | project | `/home/alex/projects/headquarter/.claude/skills/sift-backlog/SKILL.md` |
-
-## Loading protocol
-
-1. Match task context and target files against the `Trigger / description` column.
-2. Pass only the matching `Path` values to the subagent under `## Skills to load before work`.
-3. Instruct the subagent to read those exact `SKILL.md` files before reading, writing, reviewing, testing, or creating artifacts.
-4. If no matching skill exists, proceed without project skill injection and report `skill_resolution: none`.

.claude/skills/sift-backlog/SKILL.md

@@ -1,195 +0,0 @@
----
-name: sift-backlog
-description: Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open.
----
-
-# Sift Backlog
-
-Triage backlog tasks: prioritize, group into plans, set dependencies, and activate.
-
-## Overview
-
-1. List backlog tasks (`sf task backlog`)
-2. Clarify and enrich each task (titles, descriptions)
-3. Identify groupings and create draft plans
-4. Add tasks to plans and set dependencies
-5. Activate plans
-6. Set task status to open
-
-## Workflow
-
-### Step 1: List Backlog Tasks
-
-```bash
-sf task backlog
-```
-
-### Step 2: Clarify and Enrich Tasks
-
-Backlog tasks often have only a brief title with no description. Before organizing, ensure each task is well-defined.
-
-**For each task, evaluate:**
-
-- Is the title clear and actionable?
-- Is there a description? Check with `sf task describe <task-id> --show`
-- Is the scope unambiguous?
-
-**If the title is unclear**, update it:
-
-```bash
-sf update <task-id> --title "Clear, actionable title"
-```
-
-**Add a description** with context, scope, and acceptance criteria:
-
-```bash
-sf task describe <task-id> --content "Description with:
-- What needs to be done
-- Why it matters
-- Acceptance criteria
-- Any relevant context"
-```
-
-**Use your best judgment** to interpret tasks and make reasonable decisions about scope, grouping, and priority. You have context about the codebase, project patterns, and typical development practices—leverage this knowledge rather than deferring to the user for routine decisions.
-
-**Only ask the user for clarity when absolutely necessary:**
-
-- The task is fundamentally ambiguous (multiple mutually exclusive interpretations)
-- Critical business logic or user-facing behavior that could go wrong in meaningful ways
-- External dependencies or integrations you cannot verify
-
-**Do NOT ask about:**
-
-- Implementation details you can reasonably infer
-- Priority or grouping decisions—use your judgment
-- Standard development practices (testing, code style, etc.)
-- Tasks where a reasonable interpretation exists
-
-### Step 3: Create Draft Plans
-
-Group related tasks into plans using your best judgment. Plans start as drafts (tasks won't be dispatched until activated).
-
-**Grouping guidance:**
-
-- Group tasks that share a common theme, feature area, or goal
-- Consider technical dependencies when grouping (tasks that touch the same files/modules)
-- Separate unrelated work into distinct plans for parallel execution
-- Don't over-group—if tasks are truly independent, separate plans enable better parallelism
-- Don't under-group—related tasks benefit from shared context and coordinated execution
-
-```bash
-sf plan create --title "Plan Name"
-```
-
-**Example:**
-
-```bash
-sf plan create --title "Authentication Improvements"
-# Output: Created plan el-abc123
-```
-
-### Step 4: Add Tasks to Plans
-
-```bash
-sf plan add-task <plan-id> <task-id>
-```
-
-**Example:**
-
-```bash
-sf plan add-task el-abc123 el-task1
-sf plan add-task el-abc123 el-task2
-```
-
-### Step 5: Set Dependencies Between Tasks
-
-Use `blocks` dependency when one task must complete before another can start.
-
-```bash
-sf dependency add <blocked-id> <blocker-id> --type blocks
-```
-
-**Semantics:** The first ID is blocked BY the second ID. The blocker must complete first.
-
-**Example:** Task 2 can't start until Task 1 completes:
-
-```bash
-sf dependency add el-task2 el-task1 --type blocks
-```
-
-### Step 6: Update Priorities
-
-Set priorities based on your assessment of impact, urgency, and dependencies. Use your judgment—you don't need user confirmation for routine prioritization.
-
-**Priority guidance:**
-
-- **Critical (1):** Blocking issues, security vulnerabilities, production bugs
-- **High (2):** Important features with deadlines, significant user impact
-- **Medium (3):** Standard feature work, most tasks default here
-- **Low (4):** Nice-to-haves, minor improvements, tech debt
-- **Minimal (5):** Backlog cleanup, documentation, exploratory work
-
-```bash
-sf update <task-id> --priority <1-5>
-```
-
-| Value | Level    |
-| ----- | -------- |
-| 1     | Critical |
-| 2     | High     |
-| 3     | Medium   |
-| 4     | Low      |
-| 5     | Minimal  |
-
-### Step 7: Activate Plans
-
-Once tasks are organized with dependencies set, activate plans to enable dispatch.
-
-```bash
-sf plan activate <plan-id>
-```
-
-### Step 8: Set Task Status to Open
-
-Move tasks from backlog to open so they become ready for work.
-
-```bash
-sf update <id> --status open
-```
-
-## Other Actions
-
-**Close obsolete tasks:**
-
-```bash
-sf task close <id> --reason "Won't do: <reason>"
-```
-
-**Defer tasks:**
-
-```bash
-sf task defer <id> --until <date>
-```
-
-**View existing plans:**
-
-```bash
-sf plan list
-```
-
-**View tasks in a plan:**
-
-```bash
-sf plan tasks <plan-id>
-```
-
-## Tips
-
-- **Use your best judgment** for grouping, prioritization, and task interpretation—don't defer routine decisions to the user
-- **Only escalate to the user** when ambiguity is fundamental and could lead to wasted work (mutually exclusive interpretations, critical business decisions)
-- Make reasonable inferences about implementation details, scope, and priority based on codebase context
-- Create plans before setting dependencies to avoid dispatch race conditions
-- Always activate plans after dependencies are set
-- Focus on oldest backlog items first (sorted by creation date)
-- Every task should have a clear title and description before activation
-- When uncertain about a minor detail, make a reasonable choice and document it in the task description—workers can ask if needed

.pi/settings.json

@@ -1 +0,0 @@
-{}

.sisyphus/run-continuation/ses_1da2608b1ffergOzow3NQt1mGr.json

@@ -1,10 +0,0 @@
-{
-  "sessionID": "ses_1da2608b1ffergOzow3NQt1mGr",
-  "updatedAt": "2026-05-15T23:50:42.832Z",
-  "sources": {
-    "background-task": {
-      "state": "idle",
-      "updatedAt": "2026-05-15T23:50:42.832Z"
-    }
-  }
-}

.stoneforge/.dashboard-opened

@@ -1,2 +0,0 @@
-262629
-1779624255076

.stoneforge/.gitignore

@@ -1,6 +0,0 @@
-# Runtime data
-*.db
-*.db-journal
-*.db-wal
-*.db-shm
-daemon-state.json

.stoneforge/config.yaml

@@ -1,20 +0,0 @@
-# Stoneforge Configuration
-
-database: stoneforge.db
-sync:
-  auto_export: true
-  elements_file: elements.jsonl
-  dependencies_file: dependencies.jsonl
-playbooks:
-  paths:
-    - playbooks
-identity:
-  mode: soft
-merge:
-  auto_merge: true
-  target_branch: null
-  require_approval: false
-workflow:
-  preset: auto
-agents:
-  permission_model: unrestricted

.stoneforge/sync/dependencies.jsonl

@@ -1,43 +0,0 @@
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-{"blockedId":"el-5z8","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.490Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.607Z","createdBy":"el-2jua"}
-{"blockedId":"el-5j5","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.726Z","createdBy":"el-2jua"}
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-{"blockedId":"el-4bc","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.959Z","createdBy":"el-2jua"}
-{"blockedId":"el-107","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.074Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.195Z","createdBy":"el-2jua"}
-{"blockedId":"el-3ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.311Z","createdBy":"el-2jua"}
-{"blockedId":"el-14w","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.425Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.541Z","createdBy":"el-2jua"}
-{"blockedId":"el-1nj","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.651Z","createdBy":"el-2jua"}
-{"blockedId":"el-1bn","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.761Z","createdBy":"el-2jua"}
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-{"blockedId":"el-62c","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:42.979Z","createdBy":"el-2jua"}
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-{"blockedId":"el-3ou","blockerId":"el-4bc","type":"blocks","createdAt":"2026-05-24T12:44:44.650Z","createdBy":"el-2jua"}
-{"blockedId":"el-3ou","blockerId":"el-107","type":"blocks","createdAt":"2026-05-24T12:44:44.761Z","createdBy":"el-2jua"}
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AGENTS.md

@@ -85,13 +85,6 @@ Before completion, report:
 
 Do not claim completion without verification evidence.
 
-## Git branch policy
-
-- **Default working branch:** `dev` — all commits and pushes target `dev` unless the user explicitly requests otherwise.
-- `main` is the stable/production branch; merge to `main` only when explicitly instructed.
-- After committing, push to `origin/dev`.
-- If `dev` does not exist locally, create it from `main` or fetch it from origin.
-
 ## Git workflow
 
 ### Auto-commit on spec completion

apps/api/.pi-lens/cache/python-rules-v2.json

@@ -1,568 +0,0 @@
-{
-  "version": "v2",
-  "timestamp": 1779889907001,
-  "ruleHash": "fd9b2b15f2ac8993",
-  "queries": [
-    {
-      "id": "bare-except",
-      "name": "Bare Except Clause",
-      "severity": "warning",
-      "language": "python",
-      "message": "Bare 'except:' clause — catches SystemExit, KeyboardInterrupt",
-      "query": "  (except_clause\n    \"except\") @CLAUSE",
-      "metavars": [
-        "CLAUSE"
-      ],
-      "post_filter": "bare_except_only",
-      "defect_class": "silent-error",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/bare-except.yml"
-    },
-    {
-      "id": "eval-exec",
-      "name": "Eval/Exec Usage",
-      "severity": "warning",
-      "language": "python",
-      "message": "{{FUNC}}() detected — security risk, code injection vulnerability",
-      "query": "  (call\n    function: (identifier) @FUNC\n    (#match? @FUNC \"^(eval|exec)$\")\n    arguments: (argument_list) @ARGS)",
-      "metavars": [
-        "FUNC",
-        "ARGS"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/eval-exec.yml"
-    },
-    {
-      "id": "exit-signature-check",
-      "name": "__exit__ Missing Parameters",
-      "severity": "error",
-      "language": "python",
-      "message": "__exit__ should accept type, value, and traceback arguments",
-      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__exit__\")\n    parameters: (parameters\n      (_) @SELF\n      . (_) @PARAM1?\n      . (_) @PARAM2?\n      . (_) @PARAM3?))",
-      "metavars": [
-        "NAME",
-        "SELF",
-        "PARAM1",
-        "PARAM2",
-        "PARAM3"
-      ],
-      "post_filter": "exit_params_insufficient",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/exit-signature-check.yml"
-    },
-    {
-      "id": "in-operator-unsupported",
-      "name": "In and Not In Operators Should Be Used on Valid Objects",
-      "severity": "warning",
-      "language": "python",
-      "message": "'in' operator used on object that may not support containment",
-      "query": "  (comparison_operator\n    (identifier) @OBJ\n    \"in\"\n    (identifier) @TARGET)\n  (comparison_operator\n    (identifier) @OBJ\n    \"not\"\n    \"in\"\n    (identifier) @TARGET)",
-      "metavars": [
-        "OBJ",
-        "TARGET"
-      ],
-      "post_filter": "check_in_operator_types",
-      "defect_class": "correctness",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/in-operator-unsupported.yml"
-    },
-    {
-      "id": "is-vs-equals",
-      "name": "Is vs Equals for Literals",
-      "severity": "warning",
-      "language": "python",
-      "message": "Using 'is' with literal — use '==' for value comparison",
-      "query": "  (comparison_operator\n    (identifier)\n    (\"is\")\n    (string) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is not\")\n    (string) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is\")\n    (integer) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is not\")\n    (integer) @LITERAL)",
-      "metavars": [
-        "LITERAL"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/is-vs-equals.yml"
-    },
-    {
-      "id": "iter-return-iterator",
-      "name": "__iter__ Should Return Iterator",
-      "severity": "warning",
-      "language": "python",
-      "message": "__iter__ should return an iterator (object with __next__ method)",
-      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__iter__\")\n    body: (block\n      (return_statement) @RETURN))",
-      "metavars": [
-        "NAME",
-        "RETURN"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/iter-return-iterator.yml"
-    },
-    {
-      "id": "mutable-default-arg",
-      "name": "Mutable Default Argument",
-      "severity": "warning",
-      "language": "python",
-      "message": "Mutable default argument — list/dict/set as default value",
-      "query": "  (function_definition\n    (parameters\n      (default_parameter\n        (identifier) @PARAM\n        [(list) (dictionary) (set)] @MUTABLE)))",
-      "metavars": [
-        "PARAM",
-        "MUTABLE"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/mutable-default-arg.yml"
-    },
-    {
-      "id": "no-super-torchscript",
-      "name": "super Should Not Be Used in TorchScript Methods",
-      "severity": "error",
-      "language": "python",
-      "message": "super() calls should not be used in TorchScript methods",
-      "query": "  (function_definition\n    (decorator\n      (call\n        function: (identifier) @DEC (#match? @DEC \"^(torch\\.jit\\.script|jit\\.script)$\")))\n    body: (block\n      (call\n        function: (identifier) @FUNC (#eq? @FUNC \"super\")) @CALL))",
-      "metavars": [
-        "DEC",
-        "FUNC",
-        "CALL"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/no-super-torchscript.yml"
-    },
-    {
-      "id": "notimplemented-boolean-context",
-      "name": "NotImplemented in Boolean Context",
-      "severity": "error",
-      "language": "python",
-      "message": "NotImplemented should not be used in boolean contexts",
-      "query": "  (if_statement\n    condition: (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (while_statement\n    condition: (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (binary_operator\n    (identifier) @COND (#eq? @COND \"NotImplemented\")\n    (\"and\" | \"or\"))\n  (boolean_operator\n    (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (unary_operator\n    operator: (\"not\")\n    argument: (identifier) @COND (#eq? @COND \"NotImplemented\"))",
-      "metavars": [
-        "COND"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/notimplemented-boolean-context.yml"
-    },
-    {
-      "id": "python-assert-production",
-      "name": "Assert in Production Code",
-      "severity": "warning",
-      "language": "python",
-      "message": "assert statement stripped by Python -O flag — use explicit checks with exceptions in production code",
-      "query": "  (assert_statement) @ASSERT",
-      "metavars": [
-        "ASSERT"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-assert-production.yml"
-    },
-    {
-      "id": "python-command-injection",
-      "name": "Command Injection Sink",
-      "severity": "error",
-      "language": "python",
-      "message": "Potential command injection sink — avoid shell execution with dynamic input",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"os\")\n    (#match? @FN \"^(system|popen)$\"))\n\n  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      (keyword_argument\n        name: (identifier) @KW\n        value: (true)))\n    (#eq? @MOD \"subprocess\")\n    (#match? @FN \"^(run|Popen|call|check_output|check_call)$\")\n    (#eq? @KW \"shell\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "ARGS",
-        "KW"
-      ],
-      "post_filter": "py_command_injection_sink",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-command-injection.yml"
-    },
-    {
-      "id": "python-cross-language-method",
-      "name": "Cross-Language Method Leakage",
-      "severity": "warning",
-      "language": "python",
-      "message": "'{METHOD}' is not a Python method — likely a {LANG} idiom leaking in",
-      "query": "  (call\n    function: (attribute\n      object: (_) @OBJ\n      attribute: (identifier) @METHOD)\n    (#match? @METHOD \"^(push|forEach|indexOf|charAt|substring|hasOwnProperty|unshift|flatMap|padStart|padEnd|trimStart|trimEnd|equals|isEmpty|println|printf|getClass|hashCode|toCharArray|getBytes|compareTo|equalsIgnoreCase|startsWith|endsWith|each|collect|select|reject|detect|inject|chomp|chop|gsub|upcase|downcase|present|blank|Add|Contains|ToLower|ToUpper|Trim|Substring|WriteLine|ReadLine|TryParse|forEach|includes|assign|freeze|splice|unshift|shift|flatMap)$\"))",
-      "metavars": [
-        "OBJ",
-        "METHOD"
-      ],
-      "post_filter": "match_captures",
-      "post_filter_params": {
-        "METHOD": "^(push|forEach|indexOf|charAt|substring|hasOwnProperty|unshift|flatMap|padStart|padEnd|trimStart|trimEnd|equals|isEmpty|println|printf|getClass|hashCode|toCharArray|getBytes|compareTo|equalsIgnoreCase|startsWith|endsWith|each|collect|select|reject|detect|inject|chomp|chop|gsub|upcase|downcase|present|blank|Add|Contains|ToLower|ToUpper|Trim|Substring|WriteLine|ReadLine|TryParse|forEach|includes|assign|freeze|splice|unshift|shift|flatMap)$"
-      },
-      "defect_class": "hallucination",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-cross-language-method.yml"
-    },
-    {
-      "id": "python-debugger",
-      "name": "Debugger Statement",
-      "severity": "warning",
-      "language": "python",
-      "message": "Debugger call '{{FUNC}}' — remove before committing",
-      "query": "  (call\n    function: (identifier) @FUNC\n    (#eq? @FUNC \"breakpoint\"))\n\n  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FUNC)\n    (#eq? @MOD \"pdb\")\n    (#match? @FUNC \"^(set_trace|post_mortem|pm|run|runcall)$\"))",
-      "metavars": [
-        "FUNC",
-        "MOD"
-      ],
-      "defect_class": "safety",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-debugger.yml"
-    },
-    {
-      "id": "python-empty-except",
-      "name": "Empty Except Block",
-      "severity": "warning",
-      "language": "python",
-      "message": "Except block only contains 'pass' — handle or re-raise the exception",
-      "query": "  (try_statement\n    (except_clause\n      body: (block) @BODY))",
-      "metavars": [
-        "BODY"
-      ],
-      "post_filter": "python_empty_except",
-      "defect_class": "silent-error",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-empty-except.yml"
-    },
-    {
-      "id": "python-hallucinated-import",
-      "name": "Hallucinated Import",
-      "severity": "warning",
-      "language": "python",
-      "message": "Hallucinated import — '{NAME}' does not exist in '{MODULE}'",
-      "query": "  (import_from_statement\n    module_name: (dotted_name) @MODULE\n    name: (dotted_name) @NAME)",
-      "metavars": [
-        "MODULE",
-        "NAME"
-      ],
-      "post_filter": "match_captures",
-      "post_filter_params": {
-        "MODULE": "^(requests|flask|django|typing|collections|asyncio|json|unittest|pytest|urllib|sqlalchemy)$",
-        "NAME": "^(JSONResponse|HTMLResponse|RedirectResponse|StreamingResponse|Depends|Query|Path|Body|Header|Cookie|Form|File|UploadFile|FastAPI|APIRouter|HTTPException|BackgroundTasks|dataclass|fields|BaseModel|Field|validator|aiohttp|parse|stringify|fixture|TestCase|get|post|put|delete|Model|Session|Column|Integer|String)$"
-      },
-      "defect_class": "hallucination",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-hallucinated-import.yml"
-    },
-    {
-      "id": "python-hardcoded-secrets",
-      "name": "Hardcoded Secret",
-      "severity": "warning",
-      "language": "python",
-      "message": "Hardcoded {{VARNAME}} — use environment variables or a secrets manager",
-      "query": "  (assignment\n    left: (identifier) @VARNAME\n    right: (string) @VALUE)",
-      "metavars": [
-        "VARNAME",
-        "VALUE"
-      ],
-      "post_filter": "check_secret_pattern",
-      "defect_class": "secrets",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-hardcoded-secrets.yml"
-    },
-    {
-      "id": "python-insecure-deserialization",
-      "name": "Insecure Deserialization",
-      "severity": "error",
-      "language": "python",
-      "message": "Potential insecure deserialization sink — avoid unsafe loaders",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list (_) @DATA)\n    (#match? @MOD \"^(pickle|yaml)$\")\n    (#match? @FN \"^(load|loads|unsafe_load)$\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "DATA"
-      ],
-      "post_filter": "py_insecure_deserialization_sink",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-insecure-deserialization.yml"
-    },
-    {
-      "id": "python-insecure-random",
-      "name": "Insecure Randomness",
-      "severity": "warning",
-      "language": "python",
-      "message": "Insecure randomness source detected — use secrets or os.urandom for security-sensitive values",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"random\")\n    (#match? @FN \"^(random|randint|randrange|choice|choices)$\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "ARGS"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-insecure-random.yml"
-    },
-    {
-      "id": "python-mutable-class-attr",
-      "name": "Mutable Class Attribute",
-      "severity": "warning",
-      "language": "python",
-      "message": "Class attribute '{{VARNAME}}' is mutable — shared across all instances",
-      "query": "  (class_definition\n    body: (block\n      (expression_statement\n        (assignment\n          left: (identifier) @VARNAME\n          right: [\n            (list) @VALUE\n            (dictionary) @VALUE\n            (set) @VALUE\n          ]))))",
-      "metavars": [
-        "VARNAME",
-        "VALUE"
-      ],
-      "post_filter": "not_in_function",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-mutable-class-attr.yml"
-    },
-    {
-      "id": "python-path-traversal",
-      "name": "Path Traversal Risk",
-      "severity": "warning",
-      "language": "python",
-      "message": "Potential path traversal sink — sanitize and constrain file paths",
-      "query": "  [\n    (call\n      function: (identifier) @FN\n      arguments: (argument_list\n        [(identifier) (binary_operator) (call)] @PATH))\n    (call\n      function: (attribute\n        object: (identifier) @MOD\n        attribute: (identifier) @FN)\n      arguments: (argument_list\n        [(identifier) (binary_operator) (call)] @PATH))\n  ]\n  (#match? @FN \"^(open|read_text|read_bytes|write_text|write_bytes|remove|unlink|rmdir)$\")",
-      "metavars": [
-        "MOD",
-        "FN",
-        "PATH"
-      ],
-      "post_filter": "py_path_traversal_sink",
-      "defect_class": "injection",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-path-traversal.yml"
-    },
-    {
-      "id": "python-print-statement",
-      "name": "Print Statement in Production",
-      "severity": "warning",
-      "language": "python",
-      "message": "print() — remove debug output before committing",
-      "query": "  (call\n    function: (identifier) @FUNC\n    (#eq? @FUNC \"print\")\n    arguments: (argument_list) @ARGS)",
-      "metavars": [
-        "FUNC",
-        "ARGS"
-      ],
-      "post_filter": "not_in_test_block",
-      "defect_class": "safety",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-print-statement.yml"
-    },
-    {
-      "id": "python-raise-string",
-      "name": "Raise String Instead of Exception",
-      "severity": "warning",
-      "language": "python",
-      "message": "raise with string literal — Python 3 requires exception instances",
-      "query": "  (raise_statement\n    (string) @VALUE)",
-      "metavars": [
-        "VALUE"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-raise-string.yml"
-    },
-    {
-      "id": "python-sleep-in-test",
-      "name": "time.sleep in Test",
-      "severity": "warning",
-      "language": "python",
-      "message": "time.sleep() in test — use synchronisation primitives or polling helpers instead of fixed sleeps",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    (#eq? @MOD \"time\")\n    (#eq? @FN \"sleep\")) @CALL",
-      "metavars": [
-        "MOD",
-        "FN",
-        "CALL"
-      ],
-      "defect_class": "async-misuse",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-sleep-in-test.yml"
-    },
-    {
-      "id": "python-sql-injection",
-      "name": "SQL Injection Risk",
-      "severity": "error",
-      "language": "python",
-      "message": "Potential SQL injection sink — use parameterized queries",
-      "query": "  (call\n    function: (attribute\n      object: (_) @OBJ\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      [(binary_operator) (identifier) (call)] @SQL\n      (_)*))",
-      "metavars": [
-        "OBJ",
-        "FN",
-        "SQL"
-      ],
-      "post_filter": "py_sql_injection_sink",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-sql-injection.yml"
-    },
-    {
-      "id": "python-ssrf",
-      "name": "SSRF Risk",
-      "severity": "warning",
-      "language": "python",
-      "message": "Potential SSRF sink — validate/allowlist outbound URLs",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      [(identifier) (subscript) (call)] @URL)\n    (#eq? @MOD \"requests\")\n    (#match? @FN \"^(get|post|put|patch|delete|request|head|options)$\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "URL"
-      ],
-      "post_filter": "py_ssrf_sink",
-      "defect_class": "injection",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-ssrf.yml"
-    },
-    {
-      "id": "python-subprocess-shell",
-      "name": "subprocess with shell=True",
-      "severity": "warning",
-      "language": "python",
-      "message": "subprocess called with shell=True — command injection risk if any argument is user-controlled",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      (keyword_argument\n        name: (identifier) @KW\n        value: (true) @VAL))\n    (#eq? @MOD \"subprocess\")\n    (#match? @FN \"^(run|Popen|call|check_output|check_call)$\")\n    (#eq? @KW \"shell\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "KW"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-subprocess-shell.yml"
-    },
-    {
-      "id": "python-thread-global-write",
-      "name": "Threaded Shared State Risk",
-      "severity": "warning",
-      "language": "python",
-      "message": "Thread creation detected — ensure shared state mutations are synchronized",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS)\n  (#eq? @MOD \"threading\")\n  (#eq? @FN \"Thread\")",
-      "metavars": [
-        "MOD",
-        "FN",
-        "ARGS"
-      ],
-      "defect_class": "async-misuse",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-thread-global-write.yml"
-    },
-    {
-      "id": "python-unsafe-regex",
-      "name": "Unsafe Dynamic Regex",
-      "severity": "warning",
-      "language": "python",
-      "message": "re.{{FUNC}}() with variable pattern — ReDoS risk if pattern is user-controlled",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FUNC)\n    arguments: (argument_list\n      (identifier) @PATTERN)\n    (#eq? @MOD \"re\")\n    (#match? @FUNC \"^(compile|match|search|fullmatch|findall|finditer|sub|subn|split)$\"))",
-      "metavars": [
-        "MOD",
-        "FUNC",
-        "PATTERN"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-unsafe-regex.yml"
-    },
-    {
-      "id": "python-weak-hash",
-      "name": "Weak Hash Primitive",
-      "severity": "error",
-      "language": "python",
-      "message": "Weak hash primitive detected (MD5/SHA1) — use SHA-256+ for security-sensitive contexts",
-      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"hashlib\")\n    (#match? @FN \"^(md5|sha1)$\"))",
-      "metavars": [
-        "MOD",
-        "FN",
-        "ARGS"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-weak-hash.yml"
-    },
-    {
-      "id": "return-in-generator",
-      "name": "Return with Value in Generator",
-      "severity": "error",
-      "language": "python",
-      "message": "'return' with a value should not be used in a generator function",
-      "query": "  (function_definition\n    body: (block\n      (return_statement\n        (_) @RETURN_VAL) @RETURN)) @FUNCTION",
-      "metavars": [
-        "FUNCTION",
-        "RETURN",
-        "RETURN_VAL"
-      ],
-      "post_filter": "is_generator_with_valued_return",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/return-in-generator.yml"
-    },
-    {
-      "id": "return-in-init",
-      "name": "Return Value in __init__",
-      "severity": "error",
-      "language": "python",
-      "message": "__init__ should not return a value — it must always return None",
-      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__init__\")\n    body: (block\n      (return_statement\n        (_) @RETURN_VAL) @RETURN))",
-      "metavars": [
-        "NAME",
-        "RETURN",
-        "RETURN_VAL"
-      ],
-      "post_filter": "has_return_value",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/return-in-init.yml"
-    },
-    {
-      "id": "send-file-mimetype",
-      "name": "send_file Should Specify Mimetype or Download Name",
-      "severity": "error",
-      "language": "python",
-      "message": "send_file should specify 'mimetype' or 'download_name' when used with file-like objects",
-      "query": "  (call\n    function: (identifier) @FUNC (#eq? @FUNC \"send_file\")\n    arguments: (argument_list\n      (_) @FIRST_ARG\n      (keyword_argument)? @KW))",
-      "metavars": [
-        "FUNC",
-        "FIRST_ARG",
-        "KW"
-      ],
-      "post_filter": "missing_mimetype_and_download_name",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/send-file-mimetype.yml"
-    },
-    {
-      "id": "unreachable-except",
-      "name": "Unreachable Except Clause",
-      "severity": "warning",
-      "language": "python",
-      "message": "Unreachable except clause — earlier except catches all",
-      "query": "  (try_statement\n    (except_clause\n      \"except\") @GENERAL\n    (except_clause\n      \"except\"\n      (identifier) @SPECIFIC))",
-      "metavars": [
-        "GENERAL",
-        "SPECIFIC"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/unreachable-except.yml"
-    },
-    {
-      "id": "wildcard-import",
-      "name": "Wildcard Import",
-      "severity": "warning",
-      "language": "python",
-      "message": "Wildcard import — pollutes namespace, hard to track origin",
-      "query": "  (import_from_statement\n    module_name: (dotted_name) @MODULE\n    (wildcard_import) @WILDCARD)",
-      "metavars": [
-        "MODULE",
-        "WILDCARD"
-      ],
-      "defect_class": "safety",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/wildcard-import.yml"
-    },
-    {
-      "id": "yield-return-outside-function",
-      "name": "Yield/Return Outside Function",
-      "severity": "error",
-      "language": "python",
-      "message": "{{STATEMENT}} used outside function — syntax error",
-      "query": "  (module\n    (expression_statement\n      (yield) @STATEMENT))\n  (module\n    (expression_statement\n      (yield_expression) @STATEMENT))\n  (module\n    (return_statement) @STATEMENT)",
-      "metavars": [
-        "STATEMENT"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/yield-return-outside-function.yml"
-    }
-  ]
-}

apps/api/alembic/versions/0013_add_probe_result.py

@@ -1,29 +0,0 @@
-"""add probe_result to tool_instances
-
-Revision ID: 0013_add_probe_result
-Revises: 0012_default_port_req
-Create Date: 2026-05-22 21:45:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "0013_add_probe_result"
-down_revision: Union[str, None] = "0012_default_port_req"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "tool_instances",
-        sa.Column("probe_result", postgresql.JSON, nullable=True)
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("tool_instances", "probe_result")

apps/api/alembic/versions/0014_merge_heads.py

@@ -1,23 +0,0 @@
-"""merge migration heads
-
-Revision ID: 0014_merge_heads
-Revises: 0013_add_probe_result, 8ed7dd80973d
-Create Date: 2026-05-22 21:50:00.000000
-
-"""
-from typing import Sequence, Union
-
-
-# revision identifiers, used by Alembic.
-revision: str = "0014_merge_heads"
-down_revision: Union[str, Sequence[str], None] = ("0013_add_probe_result", "8ed7dd80973d")
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/0015_single_interface.py

@@ -1,109 +0,0 @@
-"""replace interfaces with interface_type and add requires_port
-
-Revision ID: 0015_single_interface
-Revises: 0014_merge_heads
-Create Date: 2026-05-22 22:00:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "0015_single_interface"
-down_revision: Union[str, Sequence[str], None] = "0014_merge_heads"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def _get_dialect() -> str:
-    """Get the current database dialect name."""
-    conn = op.get_bind()
-    return conn.dialect.name
-
-
-def upgrade() -> None:
-    dialect = _get_dialect()
-    
-    # Add new columns
-    op.add_column('tool_types', sa.Column('interface_type', sa.String(20), nullable=True))
-    op.add_column('tool_types', sa.Column('requires_port', sa.Boolean(), nullable=False, server_default='true'))
-    
-    # Migrate data: take first element from interfaces JSON array
-    if dialect == 'postgresql':
-        op.execute("""
-            UPDATE tool_types 
-            SET interface_type = COALESCE(
-                (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
-                'web'
-            ),
-            requires_port = CASE 
-                WHEN COALESCE(
-                    (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
-                    'web'
-                ) = 'web' THEN true
-                ELSE false
-            END
-        """)
-    else:
-        # SQLite: interfaces is stored as JSON text, extract first array element
-        op.execute("""
-            UPDATE tool_types 
-            SET interface_type = COALESCE(
-                (SELECT json_extract(value, '$[0]') 
-                 FROM json_each(interfaces) AS value 
-                 WHERE json_valid(interfaces) 
-                 LIMIT 1),
-                'web'
-            ),
-            requires_port = CASE 
-                WHEN COALESCE(
-                    (SELECT json_extract(value, '$[0]') 
-                     FROM json_each(interfaces) AS value 
-                     WHERE json_valid(interfaces) 
-                     LIMIT 1),
-                    'web'
-                ) = 'web' THEN true
-                ELSE false
-            END
-        """)
-    
-    # Make interface_type non-nullable after data migration
-    op.alter_column('tool_types', 'interface_type', nullable=False)
-    
-    # Drop old interfaces column
-    op.drop_column('tool_types', 'interfaces')
-    
-    # Add CHECK constraint for interface_type (only on PostgreSQL; SQLite supports it too)
-    op.create_check_constraint('chk_interface_type', 'tool_types', sa.text("interface_type IN ('web', 'terminal')"))
-
-
-def downgrade() -> None:
-    dialect = _get_dialect()
-    
-    # Drop CHECK constraint
-    op.drop_constraint('chk_interface_type', 'tool_types', type_='check')
-    
-    # Add back interfaces column
-    if dialect == 'postgresql':
-        op.add_column('tool_types', sa.Column('interfaces', postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='["web"]'))
-        
-        # Migrate data back: wrap interface_type in array
-        op.execute("""
-            UPDATE tool_types 
-            SET interfaces = jsonb_build_array(interface_type)
-        """)
-    else:
-        op.add_column('tool_types', sa.Column('interfaces', sa.JSON(), nullable=False, server_default='["web"]'))
-        
-        # Migrate data back: wrap interface_type in array for SQLite
-        op.execute("""
-            UPDATE tool_types 
-            SET interfaces = json_array(interface_type)
-        """)
-    
-    # Drop new columns
-    op.drop_column('tool_types', 'requires_port')
-    op.drop_column('tool_types', 'interface_type')

apps/api/alembic/versions/069d3da4dc9b_add_ssh_key_id_to_config_profiles.py

@@ -1,32 +0,0 @@
-"""add_ssh_key_id_to_config_profiles
-
-Revision ID: 069d3da4dc9b
-Revises: 2026_05_29_add_notifications_table
-Create Date: 2026-05-29 12:30:16.580532
-"""
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = "069d3da4dc9b"
-down_revision = "2026_05_29_add_notifications_table"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "config_profiles",
-        sa.Column(
-            "ssh_key_id",
-            sa.Uuid(),
-            sa.ForeignKey("ssh_keys.id", ondelete="SET NULL"),
-            nullable=True,
-        ),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("config_profiles", "ssh_key_id")

apps/api/alembic/versions/20260527160017_add_pi_agent_tool_type.py

@@ -1,129 +0,0 @@
-"""add pi agent tool type
-
-Revision ID: 20260527_160017_add_pi_agent
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-27T16:00:17
-
-"""
-
-import json
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-import uuid
-
-# revision identifiers, used by Alembic.
-revision: str = "20260527_160017_add_pi_agent"
-down_revision: Union[str, None] = "2026_05_27_external_repos"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-PI_AGENT_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
-
-
-def upgrade() -> None:
-    # Check if pi-agent already exists
-    conn = op.get_bind()
-    result = conn.execute(
-        sa.text("SELECT id FROM tool_types WHERE name = 'pi-agent'")
-    ).fetchone()
-    
-    if result is None:
-        conn.execute(
-            sa.text("""
-                INSERT INTO tool_types (
-                    id, name, display_name, description, category,
-                    interface_type, requires_port, default_port,
-                    definition_type, compose_template, dockerfile_template, required_variables,
-                    created_at, updated_at
-                ) VALUES (
-                    :id, :name, :display_name, :description, :category,
-                    :interface_type, :requires_port, :default_port,
-                    :definition_type, :compose_template, :dockerfile_template, :required_variables,
-                    now(), now()
-                )
-            """),
-            {
-                "id": PI_AGENT_ID,
-                "name": "pi-agent",
-                "display_name": "Pi Agent",
-                "description": "Pi coding agent terminal environment with nvim, ranger, and tmux",
-                "category": "development",
-                "interface_type": "terminal",
-                "requires_port": False,
-                "default_port": 0,
-                "definition_type": "dockerfile",
-                "compose_template": """services:
-  app:
-    build: .
-    stdin_open: true
-    tty: true
-    volumes:
-      - ${REPO_PATH}:/workspace
-    working_dir: /workspace
-    command: /bin/bash""",
-                "dockerfile_template": """# Pi Coding Agent - Terminal-based coding harness
-FROM ubuntu:24.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Install base dependencies
-RUN apt-get update && apt-get install -y \\
-    curl \\
-    wget \\
-    git \\
-    neovim \\
-    ranger \\
-    tmux \\
-    htop \\
-    tree \\
-    jq \\
-    ca-certificates \\
-    python3 \\
-    python3-pip \\
-    build-essential \\
-    && rm -rf /var/lib/apt/lists/*
-
-# Install Node.js (required for Pi)
-RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
-    && apt-get install -y nodejs \\
-    && rm -rf /var/lib/apt/lists/*
-
-# Install Pi Coding Agent globally
-RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
-
-# Create non-root user
-RUN useradd -m -s /bin/bash user
-WORKDIR /home/user
-
-# Set up git
-RUN git config --global init.defaultBranch main \\
-    && git config --global user.email "dev@headquarter.local" \\
-    && git config --global user.name "Developer"
-
-# Create default tmux config
-RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
-
-# Create default ranger config
-RUN mkdir -p /home/user/.config/ranger \\
-    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
-
-# Set up Pi config directory
-RUN mkdir -p /home/user/.pi/agent
-
-USER user
-
-# Default to bash (Pi is invoked manually via `pi` command)
-CMD ["/bin/bash"]""",
-                "required_variables": json.dumps(["REPO_PATH"]),
-            }
-        )
-
-
-def downgrade() -> None:
-    conn = op.get_bind()
-    conn.execute(
-        sa.text("DELETE FROM tool_types WHERE name = 'pi-agent'")
-    )

apps/api/alembic/versions/2026_05_22_add_clone_mode.py

@@ -1,36 +0,0 @@
-"""add_clone_mode_and_ssh_key_id
-
-Revision ID: 2026_05_22_add_clone_mode
-Revises: 0014_merge_heads
-Create Date: 2026-05-22 20:30:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision = '2026_05_22_add_clone_mode'
-down_revision = '0015_single_interface'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # Add ssh_key_id to git_repositories
-    op.add_column('git_repositories', sa.Column('ssh_key_id', postgresql.UUID(), nullable=True))
-    op.create_foreign_key('fk_git_repositories_ssh_key', 'git_repositories', 'ssh_keys', ['ssh_key_id'], ['id'])
-    
-    # Add clone_mode and branch to tool_instances
-    op.add_column('tool_instances', sa.Column('clone_mode', sa.String(20), nullable=False, server_default='mount'))
-    op.add_column('tool_instances', sa.Column('branch', sa.String(255), nullable=True, server_default='main'))
-
-
-def downgrade() -> None:
-    # Drop columns from tool_instances
-    op.drop_column('tool_instances', 'branch')
-    op.drop_column('tool_instances', 'clone_mode')
-    
-    # Drop ssh_key_id from git_repositories
-    op.drop_constraint('fk_git_repositories_ssh_key', 'git_repositories', type_='foreignkey')
-    op.drop_column('git_repositories', 'ssh_key_id')

apps/api/alembic/versions/2026_05_23_remove_is_builtin.py

@@ -1,25 +0,0 @@
-"""remove_is_builtin_from_tool_types
-
-Revision ID: 2026_05_23_remove_is_builtin
-Revises: 2026_05_22_add_clone_mode
-Create Date: 2026-05-23 14:30:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision = '2026_05_23_remove_is_builtin'
-down_revision = 'f3d2dc90ba3a'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # Drop the is_builtin column from tool_types
-    op.execute("ALTER TABLE tool_types DROP COLUMN IF EXISTS is_builtin")
-
-
-def downgrade() -> None:
-    # Add the is_builtin column back to tool_types
-    op.add_column('tool_types', sa.Column('is_builtin', sa.Boolean(), nullable=False, server_default='false'))

apps/api/alembic/versions/2026_05_24_220141_add_startup_command.py

@@ -1,30 +0,0 @@
-"""add startup_command to tool_types
-
-Revision ID: 2026_05_24_220141
-Revises: 6fc7bfcf199f
-Create Date: 2026-05-24 22:01:41.000000
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_24_220141"
-down_revision: Union[str, Sequence[str], None] = "6fc7bfcf199f"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "tool_types",
-        sa.Column("startup_command", sa.Text(), nullable=True),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("tool_types", "startup_command")

apps/api/alembic/versions/2026_05_24_add_config_profiles.py

@@ -1,86 +0,0 @@
-"""add_config_profiles
-
-Revision ID: 2026_05_24_add_config_profiles
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-24 14:00:00.000000
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_24_add_config_profiles"
-down_revision: Union[str, Sequence[str], None] = "f3d2dc90ba3a"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    # Create config_profiles table
-    op.create_table(
-        "config_profiles",
-        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
-        sa.Column("user_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("users.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("name", sa.String(255), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("project_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("projects.id", ondelete="CASCADE"), nullable=True),
-        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True),
-        sa.Column("env_vars", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("runtime_hints", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("mounts", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="[]"),
-        sa.Column("files", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
-        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
-    )
-
-    # Create indexes for config_profiles
-    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
-    op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
-    op.create_index("idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"])
-
-    # Create config_profile_includes table
-    op.create_table(
-        "config_profile_includes",
-        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
-        sa.Column("profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
-        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_profile_includes"),
-    )
-
-    # Create indexes for config_profile_includes
-    op.create_index("idx_config_profile_includes_profile", "config_profile_includes", ["profile_id"])
-    op.create_index("idx_config_profile_includes_included", "config_profile_includes", ["included_profile_id"])
-
-    # Add selected_config_profile_id to tool_instances
-    op.add_column(
-        "tool_instances",
-        sa.Column("selected_config_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True),
-    )
-    op.create_index("idx_tool_instances_config_profile", "tool_instances", ["selected_config_profile_id"])
-
-
-def downgrade() -> None:
-    # Remove selected_config_profile_id from tool_instances
-    op.drop_index("idx_tool_instances_config_profile", table_name="tool_instances")
-    op.drop_column("tool_instances", "selected_config_profile_id")
-
-    # Drop config_profile_includes table
-    op.drop_index("idx_config_profile_includes_included", table_name="config_profile_includes")
-    op.drop_index("idx_config_profile_includes_profile", table_name="config_profile_includes")
-    op.drop_table("config_profile_includes")
-
-    # Drop config_profiles table
-    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
-    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
-    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
-    op.drop_table("config_profiles")

apps/api/alembic/versions/2026_05_26_add_git_mounts.py

@@ -1,28 +0,0 @@
-"""add_git_mounts_to_config_profiles
-
-Revision ID: 2026_05_26_add_git_mounts
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-26 12:00:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_26_add_git_mounts"
-down_revision: Union[str, Sequence[str], None] = "2026_05_24_220141"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "config_profiles",
-        sa.Column("git_mounts", sa.JSON(), nullable=True, default=list),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("config_profiles", "git_mounts")

apps/api/alembic/versions/2026_05_27_external_repos.py

@@ -1,41 +0,0 @@
-"""make_project_id_nullable_in_git_repositories
-
-Revision ID: 2026_05_27_external_repos
-Revises: 2026_05_26_add_git_mounts
-Create Date: 2026-05-27 08:30:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_27_external_repos"
-down_revision: Union[str, Sequence[str], None] = "2026_05_26_add_git_mounts"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    # Expand alembic_version version_num to avoid truncation errors
-    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(64)")
-    
-    # Make project_id nullable to allow external repositories
-    op.alter_column(
-        "git_repositories",
-        "project_id",
-        existing_type=sa.UUID(),
-        nullable=True,
-    )
-
-
-def downgrade() -> None:
-    op.alter_column(
-        "git_repositories",
-        "project_id",
-        existing_type=sa.UUID(),
-        nullable=False,
-    )
-    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(32)")

apps/api/alembic/versions/2026_05_28_add_monitoring_tables.py

@@ -1,122 +0,0 @@
-"""add monitoring tables
-
-Revision ID: 2026_05_28_add_monitoring_tables
-Revises: 2026_05_28_drop_tool_configs_and_config_folders
-Create Date: 2026-05-28
-
-"""
-
-from collections.abc import Sequence
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_28_add_monitoring_tables"
-down_revision: str | None = "2026_05_28_drop_tool_configs_and_config_folders"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    op.create_table(
-        "instance_events",
-        sa.Column("id", sa.Uuid(), nullable=False),
-        sa.Column(
-            "instance_id",
-            sa.Uuid(),
-            nullable=False,
-        ),
-        sa.Column("event_type", sa.String(length=50), nullable=False),
-        sa.Column("status", sa.String(length=50), nullable=True),
-        sa.Column("message", sa.Text(), nullable=True),
-        sa.Column("created_by", sa.Uuid(), nullable=True),
-        sa.Column(
-            "metadata",
-            sa.JSON(),
-            nullable=False,
-            server_default="{}",
-        ),
-        sa.Column(
-            "created_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.func.now(),
-            nullable=False,
-        ),
-        sa.ForeignKeyConstraint(
-            ["instance_id"],
-            ["tool_instances.id"],
-            ondelete="CASCADE",
-        ),
-        sa.ForeignKeyConstraint(
-            ["created_by"],
-            ["users.id"],
-            ondelete="SET NULL",
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )
-    op.create_index(
-        "idx_instance_events_instance_id",
-        "instance_events",
-        ["instance_id"],
-    )
-    op.create_index(
-        "idx_instance_events_created_at",
-        "instance_events",
-        ["created_at"],
-        postgresql_using="btree",
-    )
-    op.create_index(
-        "idx_instance_events_event_type",
-        "instance_events",
-        ["event_type"],
-    )
-
-    op.create_table(
-        "health_checks",
-        sa.Column("id", sa.Uuid(), nullable=False),
-        sa.Column(
-            "instance_id",
-            sa.Uuid(),
-            nullable=False,
-        ),
-        sa.Column("container_status", sa.String(length=50), nullable=True),
-        sa.Column("container_healthy", sa.Boolean(), nullable=True),
-        sa.Column("tunnel_healthy", sa.Boolean(), nullable=True),
-        sa.Column("exit_code", sa.Integer(), nullable=True),
-        sa.Column("probe_status", sa.String(length=50), nullable=True),
-        sa.Column("probe_output", sa.Text(), nullable=True),
-        sa.Column(
-            "checked_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.func.now(),
-            nullable=False,
-        ),
-        sa.ForeignKeyConstraint(
-            ["instance_id"],
-            ["tool_instances.id"],
-            ondelete="CASCADE",
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )
-    op.create_index(
-        "idx_health_checks_instance_id",
-        "health_checks",
-        ["instance_id"],
-    )
-    op.create_index(
-        "idx_health_checks_checked_at",
-        "health_checks",
-        ["checked_at"],
-        postgresql_using="btree",
-    )
-
-
-def downgrade() -> None:
-    op.drop_index("idx_health_checks_checked_at", table_name="health_checks")
-    op.drop_index("idx_health_checks_instance_id", table_name="health_checks")
-    op.drop_table("health_checks")
-    op.drop_index("idx_instance_events_event_type", table_name="instance_events")
-    op.drop_index("idx_instance_events_created_at", table_name="instance_events")
-    op.drop_index("idx_instance_events_instance_id", table_name="instance_events")
-    op.drop_table("instance_events")

apps/api/alembic/versions/2026_05_28_add_terminal_sessions_table.py

@@ -1,61 +0,0 @@
-"""add terminal_sessions table
-
-Revision ID: 2026_05_28_add_terminal_sessions
-Revises: 20260527_160017_add_pi_agent
-Create Date: 2026-05-28
-
-"""
-
-from collections.abc import Sequence
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_28_add_terminal_sessions"
-down_revision: str | None = "2026_05_28_add_tool_definition_manifests"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    op.create_table(
-        "terminal_sessions",
-        sa.Column("id", sa.UUID(), nullable=False),
-        sa.Column("instance_id", sa.UUID(), nullable=False),
-        sa.Column("name", sa.String(length=255), nullable=True),
-        sa.Column("status", sa.String(length=50), nullable=False),
-        sa.Column("last_activity_at", sa.DateTime(timezone=True), nullable=True),
-        sa.Column("closed_at", sa.DateTime(timezone=True), nullable=True),
-        sa.Column(
-            "created_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.text("now()"),
-            nullable=False,
-        ),
-        sa.Column(
-            "updated_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.text("now()"),
-            onupdate=sa.text("now()"),
-            nullable=False,
-        ),
-        sa.ForeignKeyConstraint(
-            ["instance_id"], ["tool_instances.id"], ondelete="CASCADE"
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )
-    op.create_index(
-        op.f("ix_terminal_sessions_instance_id"),
-        "terminal_sessions",
-        ["instance_id"],
-        unique=False,
-    )
-
-
-def downgrade() -> None:
-    op.drop_index(
-        op.f("ix_terminal_sessions_instance_id"),
-        table_name="terminal_sessions",
-    )
-    op.drop_table("terminal_sessions")

apps/api/alembic/versions/2026_05_28_add_tool_definition_manifests.py

@@ -1,373 +0,0 @@
-"""add tool definition manifests
-
-Revision ID: 2026_05_28_add_tool_definition_manifests
-Revises: 20260527_160017_add_pi_agent
-Create Date: 2026-05-28T11:00:00
-
-"""
-
-import json
-import uuid
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_28_add_tool_definition_manifests"
-down_revision: Union[str, None] = "20260527_160017_add_pi_agent"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-BASE_UBUNTU_ID = uuid.UUID("a1b2c3d4-e5f6-7890-abcd-ef1234567890")
-PI_AGENT_MANIFEST_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-
-    # ── Create tool_definition_manifests table ───────────────────────
-    op.create_table(
-        "tool_definition_manifests",
-        sa.Column("id", sa.UUID(), nullable=False),
-        sa.Column("name", sa.String(64), nullable=False),
-        sa.Column("display_name", sa.String(128), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("category", sa.String(64), nullable=True),
-        sa.Column("interface_type", sa.String(16), nullable=False),
-        sa.Column("base_image", sa.String(256), nullable=True),
-        sa.Column("base_definition_id", sa.UUID(), nullable=True),
-        sa.Column(
-            "base_version", sa.String(32), nullable=False, server_default="latest"
-        ),
-        sa.Column("manifest", sa.JSON(), nullable=False),
-        sa.Column("dockerfile_cache", sa.Text(), nullable=True),
-        sa.Column("compose_cache", sa.Text(), nullable=True),
-        sa.Column("version", sa.String(32), nullable=False, server_default="v1"),
-        sa.Column("is_base", sa.Boolean(), nullable=False, server_default="false"),
-        sa.Column("created_by_id", sa.UUID(), nullable=True),
-        sa.Column(
-            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.Column(
-            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("name"),
-        sa.ForeignKeyConstraint(
-            ["base_definition_id"], ["tool_definition_manifests.id"]
-        ),
-        sa.ForeignKeyConstraint(["created_by_id"], ["users.id"]),
-        sa.CheckConstraint(
-            "(base_image IS NOT NULL) OR (base_definition_id IS NOT NULL)",
-            name="ck_tool_definition_manifests_base_required",
-        ),
-    )
-
-    # ── Add columns to tool_types ────────────────────────────────────
-    # Check if manifest_id exists before adding
-    conn = op.get_bind()
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column("tool_types", sa.Column("manifest_id", sa.UUID(), nullable=True))
-        op.create_foreign_key(
-            "fk_tool_types_manifest_id",
-            "tool_types",
-            "tool_definition_manifests",
-            ["manifest_id"],
-            ["id"],
-        )
-
-    # Update definition_type to allow 'legacy' and 'manifest'
-    result = conn.execute(
-        sa.text("""
-            SELECT constraint_name FROM information_schema.check_constraints
-            WHERE constraint_name = 'chk_definition_type'
-        """)
-    )
-    if result.fetchone():
-        op.drop_constraint("chk_definition_type", "tool_types", type_="check")
-
-    op.execute("ALTER TABLE tool_types ALTER COLUMN definition_type TYPE VARCHAR(16)")
-    op.execute(
-        "ALTER TABLE tool_types ALTER COLUMN definition_type SET DEFAULT 'legacy'"
-    )
-
-    # ── Add columns to tool_instances ────────────────────────────────
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column(
-            "tool_instances",
-            sa.Column(
-                "manifest_compiled_at", sa.TIMESTAMP(timezone=True), nullable=True
-            ),
-        )
-
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column(
-            "tool_instances",
-            sa.Column("image_tag", sa.String(256), nullable=True),
-        )
-
-    # ── Data migration: create base definition + pi-agent manifest ───
-    conn.execute(
-        sa.text(
-            """
-            INSERT INTO tool_definition_manifests
-            (id, name, display_name, description, interface_type, base_image,
-             manifest, is_base, version, created_at, updated_at)
-            VALUES
-            (:base_id, 'ubuntu-24.04-dev', 'Ubuntu 24.04 Dev Base',
-             'Base development environment with build tools', 'terminal',
-             'ubuntu:24.04', :base_manifest, true, 'v1', now(), now())
-        """
-        ),
-        {
-            "base_id": BASE_UBUNTU_ID,
-            "base_manifest": json.dumps(
-                {
-                    "name": "ubuntu-24.04-dev",
-                    "display_name": "Ubuntu 24.04 Dev Base",
-                    "interface_type": "terminal",
-                    "base_image": "ubuntu:24.04",
-                    "packages": {
-                        "apt": [
-                            "curl",
-                            "wget",
-                            "git",
-                            "build-essential",
-                            "ca-certificates",
-                            "python3",
-                            "python3-pip",
-                        ]
-                    },
-                    "user": {
-                        "name": "user",
-                        "uid": 1000,
-                        "gid": 1000,
-                        "create_home": True,
-                        "shell": "/bin/bash",
-                    },
-                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
-                }
-            ),
-        },
-    )
-
-    conn.execute(
-        sa.text(
-            """
-            INSERT INTO tool_definition_manifests
-            (id, name, display_name, description, category, interface_type,
-             base_definition_id, base_version, manifest, version, created_at, updated_at)
-            VALUES
-            (:manifest_id, 'pi-agent', 'Pi Agent',
-             'Terminal-based coding harness with nvim, ranger, tmux',
-             'development', 'terminal', :base_id, 'v1', :manifest, 'v1',
-             now(), now())
-        """
-        ),
-        {
-            "manifest_id": PI_AGENT_MANIFEST_ID,
-            "base_id": BASE_UBUNTU_ID,
-            "manifest": json.dumps(
-                {
-                    "name": "pi-agent",
-                    "display_name": "Pi Agent",
-                    "description": "Terminal-based coding harness",
-                    "category": "development",
-                    "interface_type": "terminal",
-                    "base_definition_id": str(BASE_UBUNTU_ID),
-                    "base_version": "v1",
-                    "packages": {
-                        "apt": [
-                            "neovim",
-                            "ranger",
-                            "tmux",
-                            "htop",
-                            "tree",
-                            "jq",
-                        ],
-                        "node": {"version": "20"},
-                        "npm_global": ["@earendil-works/pi-coding-agent"],
-                    },
-                    "user": {
-                        "name": "user",
-                        "uid": 1001,
-                        "gid": 1001,
-                        "create_home": True,
-                        "shell": "/bin/bash",
-                    },
-                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
-                    "scripts": {
-                        "build": [
-                            "git config --global init.defaultBranch main && git config --global user.email 'dev@headquarter.local' && git config --global user.name 'Developer'",
-                            "mkdir -p /home/user/.config/ranger && echo 'set preview_files true' > /home/user/.config/ranger/rc.conf",
-                        ],
-                        "startup": [
-                            "if [ -d /workspace ]; then sudo chown -R user:user /workspace 2>/dev/null || true; fi",
-                        ],
-                    },
-                    "mounts": [
-                        {
-                            "name": "workspace",
-                            "target": "/workspace",
-                            "source_type": "repo",
-                            "writable": True,
-                            "owner": "user",
-                        },
-                        {
-                            "name": "pi_state",
-                            "target": "/tmp/.pi/agents",
-                            "source_type": "instance",
-                            "writable": True,
-                        },
-                        {
-                            "name": "pi_config",
-                            "target": "/home/user/.pi",
-                            "source_type": "git_mount",
-                            "git_mount_ref": "dotfiles",
-                            "writable": True,
-                            "owner": "user",
-                        },
-                    ],
-                    "runtime": {
-                        "command": ["/bin/bash"],
-                        "stdin_open": True,
-                        "tty": True,
-                        "working_dir": "/workspace",
-                    },
-                }
-            ),
-        },
-    )
-
-    # ── Update existing pi-agent tool_type ───────────────────────────
-    conn.execute(
-        sa.text(
-            """
-            UPDATE tool_types
-            SET manifest_id = :manifest_id,
-                definition_type = 'manifest',
-                dockerfile_template = NULL,
-                compose_template = NULL
-            WHERE name = 'pi-agent'
-        """
-        ),
-        {"manifest_id": PI_AGENT_MANIFEST_ID},
-    )
-
-
-def downgrade() -> None:
-    conn = op.get_bind()
-
-    # Restore pi-agent templates if manifest_id column exists
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
-        """)
-    )
-    has_manifest_id = result.fetchone() is not None
-
-    if has_manifest_id:
-        conn.execute(
-            sa.text(
-                """
-                UPDATE tool_types
-                SET manifest_id = NULL,
-                    definition_type = 'dockerfile',
-                    dockerfile_template = :dockerfile,
-                    compose_template = :compose
-                WHERE name = 'pi-agent'
-            """
-            ),
-            {
-                "dockerfile": """# Pi Coding Agent - Terminal-based coding harness
-FROM ubuntu:24.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update && apt-get install -y \\
-    curl wget git neovim ranger tmux htop tree jq \\
-    ca-certificates python3 python3-pip build-essential \\
-    && rm -rf /var/lib/apt/lists/*
-
-RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
-    && apt-get install -y nodejs \\
-    && rm -rf /var/lib/apt/lists/*
-
-RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
-
-RUN useradd -m -s /bin/bash user
-WORKDIR /home/user
-
-RUN git config --global init.defaultBranch main \\
-    && git config --global user.email "dev@headquarter.local" \\
-    && git config --global user.name "Developer"
-
-RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
-
-RUN mkdir -p /home/user/.config/ranger \\
-    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
-
-RUN mkdir -p /home/user/.pi/agent
-
-USER user
-
-CMD ["/bin/bash"]
-""",
-                "compose": """services:
-  app:
-    build: .
-    stdin_open: true
-    tty: true
-    volumes:
-      - ${REPO_PATH}:/workspace
-    working_dir: /workspace
-    command: /bin/bash""",
-            },
-        )
-
-    # Drop columns conditionally
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
-        """)
-    )
-    if result.fetchone():
-        op.drop_column("tool_instances", "image_tag")
-
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
-        """)
-    )
-    if result.fetchone():
-        op.drop_column("tool_instances", "manifest_compiled_at")
-
-    if has_manifest_id:
-        op.drop_constraint(
-            "fk_tool_types_manifest_id", "tool_types", type_="foreignkey"
-        )
-        op.drop_column("tool_types", "manifest_id")
-
-    op.drop_table("tool_definition_manifests")

apps/api/alembic/versions/2026_05_28_drop_tool_configs_and_config_folders.py

@@ -1,89 +0,0 @@
-"""drop tool_configs and config_folders tables
-
-Revision ID: 2026_05_28_drop_tool_configs_and_config_folders
-Revises: 2026_05_28_add_tool_definition_manifests
-Create Date: 2026-05-28
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_28_drop_tool_configs_and_config_folders"
-down_revision: Union[str, None] = "2026_05_28_add_terminal_sessions"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-
-    # Drop tool_configs table if it exists
-    result = conn.execute(
-        sa.text("""
-            SELECT table_name FROM information_schema.tables
-            WHERE table_name = 'tool_configs'
-        """)
-    )
-    if result.fetchone():
-        op.drop_table("tool_configs")
-
-    # Drop config_folders table if it exists
-    result = conn.execute(
-        sa.text("""
-            SELECT table_name FROM information_schema.tables
-            WHERE table_name = 'config_folders'
-        """)
-    )
-    if result.fetchone():
-        op.drop_table("config_folders")
-
-
-def downgrade() -> None:
-    # Recreate config_folders table
-    op.create_table(
-        "config_folders",
-        sa.Column("id", sa.UUID(), nullable=False),
-        sa.Column("user_id", sa.UUID(), nullable=False),
-        sa.Column("name", sa.String(255), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("mount_path", sa.String(1024), nullable=False),
-        sa.Column("files", sa.JSON(), default=dict, nullable=False),
-        sa.Column("project_overrides", sa.JSON(), default=dict, nullable=True),
-        sa.Column("is_active", sa.Boolean(), default=True, nullable=False),
-        sa.Column(
-            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.Column(
-            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )
-
-    # Recreate tool_configs table
-    op.create_table(
-        "tool_configs",
-        sa.Column("id", sa.UUID(), nullable=False),
-        sa.Column("user_id", sa.UUID(), nullable=False),
-        sa.Column("tool_type_id", sa.UUID(), nullable=False),
-        sa.Column("project_id", sa.UUID(), nullable=True),
-        sa.Column("key", sa.String(255), nullable=False),
-        sa.Column("value", sa.Text(), nullable=False),
-        sa.Column("config_type", sa.String(20), default="env", nullable=False),
-        sa.Column("file_path", sa.String(1024), nullable=True),
-        sa.Column("port_override", sa.Integer(), nullable=True),
-        sa.Column("start_command", sa.Text(), nullable=True),
-        sa.Column("working_directory", sa.Text(), nullable=True),
-        sa.Column("environment_variables", sa.JSON(), default=dict, nullable=True),
-        sa.Column("volumes", sa.JSON(), default=list, nullable=True),
-        sa.Column(
-            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.Column(
-            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )

apps/api/alembic/versions/2026_05_29_add_notifications_table.py

@@ -1,69 +0,0 @@
-"""add notifications table
-
-Revision ID: 2026_05_29_add_notifications_table
-Revises: 2026_05_28_add_monitoring_tables
-Create Date: 2026-05-29
-
-"""
-
-from collections.abc import Sequence
-
-import sqlalchemy as sa
-from alembic import op
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_add_notifications_table"
-down_revision: str | None = "2026_05_28_add_monitoring_tables"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    op.create_table(
-        "notifications",
-        sa.Column("id", sa.Uuid(), nullable=False),
-        sa.Column("user_id", sa.Uuid(), nullable=False),
-        sa.Column("category", sa.String(length=32), nullable=False),
-        sa.Column("severity", sa.String(length=16), nullable=False),
-        sa.Column("title", sa.String(length=255), nullable=False),
-        sa.Column("message", sa.Text(), nullable=True),
-        sa.Column("source_type", sa.String(length=64), nullable=True),
-        sa.Column("source_id", sa.Uuid(), nullable=True),
-        sa.Column(
-            "metadata",
-            sa.JSON(),
-            nullable=False,
-            server_default="{}",
-        ),
-        sa.Column("read_at", sa.DateTime(timezone=True), nullable=True),
-        sa.Column("dismissed_at", sa.DateTime(timezone=True), nullable=True),
-        sa.Column(
-            "created_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.func.now(),
-            nullable=False,
-        ),
-        sa.ForeignKeyConstraint(
-            ["user_id"],
-            ["users.id"],
-            ondelete="CASCADE",
-        ),
-        sa.PrimaryKeyConstraint("id"),
-    )
-    op.create_index(
-        "idx_notifications_user_created_at",
-        "notifications",
-        ["user_id", sa.text("created_at DESC")],
-    )
-    op.create_index(
-        "idx_notifications_user_unread",
-        "notifications",
-        ["user_id", "read_at"],
-        postgresql_where=sa.text("read_at IS NULL"),
-    )
-
-
-def downgrade() -> None:
-    op.drop_index("idx_notifications_user_unread", table_name="notifications")
-    op.drop_index("idx_notifications_user_created_at", table_name="notifications")
-    op.drop_table("notifications")

apps/api/alembic/versions/2026_05_29_add_ssh_key_ids_to_tool_instances.py

@@ -1,27 +0,0 @@
-"""add_ssh_key_ids_to_tool_instances
-
-Revision ID: 2026_05_29_add_ssh_key_ids_to_tool_instances
-Revises: 2026_05_29_drop_ssh_key_id_from_config_profiles
-Create Date: 2026-05-29 12:46:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = "2026_05_29_add_ssh_key_ids_to_tool_instances"
-down_revision = "2026_05_29_drop_ssh_key_id_from_config_profiles"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "tool_instances",
-        sa.Column("ssh_key_ids", sa.JSON(), nullable=True),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("tool_instances", "ssh_key_ids")

apps/api/alembic/versions/2026_05_29_drop_ssh_key_id_from_config_profiles.py

@@ -1,32 +0,0 @@
-"""drop_ssh_key_id_from_config_profiles
-
-Revision ID: 2026_05_29_drop_ssh_key_id_from_config_profiles
-Revises: 069d3da4dc9b
-Create Date: 2026-05-29 12:45:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = "2026_05_29_drop_ssh_key_id_from_config_profiles"
-down_revision = "069d3da4dc9b"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    op.drop_column("config_profiles", "ssh_key_id")
-
-
-def downgrade() -> None:
-    op.add_column(
-        "config_profiles",
-        sa.Column(
-            "ssh_key_id",
-            sa.Uuid(),
-            sa.ForeignKey("ssh_keys.id", ondelete="SET NULL"),
-            nullable=True,
-        ),
-    )

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr.py

@@ -1,54 +0,0 @@
-"""fix code-server bind-addr to host in DB template
-
-Revision ID: 2026_05_29_fix_code_server_bind_addr
-Revises: 2026_05_29_fix_web_tool_bind_address
-Create Date: 2026-05-29 15:00:00.000000
-
-"""
-
-from typing import Sequence
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_fix_code_server_bind_addr"
-down_revision: str | None = "2026_05_29_fix_web_tool_bind_address"
-branch_labels: Sequence[str] | None = None
-depends_on: Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-
-    # Find code-server tool types with broken --bind-addr in compose template
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_template
-            FROM tool_types
-            WHERE name = 'code-server'
-            AND compose_template LIKE '%--bind-addr%'
-        """)
-    ).fetchall()
-
-    for tool_id, compose_template in result:
-        updated = compose_template.replace(
-            "--bind-addr 0.0.0.0:8443", "--host 0.0.0.0"
-        ).replace("--bind-addr", "--host 0.0.0.0")
-
-        conn.execute(
-            sa.text("""
-                UPDATE tool_types
-                SET compose_template = :compose_template
-                WHERE id = :id
-            """),
-            {"compose_template": updated, "id": tool_id},
-        )
-
-        print(
-            f"Fixed code-server template ({tool_id}): replaced --bind-addr with --host"
-        )
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr_port.py

@@ -1,148 +0,0 @@
-"""Fix code-server bind address to include port
-
-Revision ID: 2026_05_29_fix_code_server_bind_addr_port
-Revises: 2026_05_29_remove_lsio_command_override
-Create Date: 2026-05-29 18:00:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-import yaml
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_fix_code_server_bind_addr_port"
-down_revision: Union[str, None] = "2026_05_29_remove_lsio_command_override"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def _fix_tool_type_templates(conn) -> None:
-    """Fix code-server tool type templates with broken --host override."""
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_template, default_port
-            FROM tool_types
-            WHERE name = 'code-server'
-            AND compose_template LIKE '%--host%'
-        """)
-    ).fetchall()
-
-    for tool_id, compose_template, default_port in result:
-        port = default_port or 8443
-        expected = f"--bind-addr 0.0.0.0:{port}"
-
-        # Replace any line containing --host with the correct bind-addr
-        lines = compose_template.split("\n")
-        new_lines = []
-        modified = False
-        for line in lines:
-            if "command:" in line and "--host" in line:
-                indent = line[: len(line) - len(line.lstrip())]
-                new_lines.append(f"{indent}command: {expected}")
-                modified = True
-            else:
-                new_lines.append(line)
-
-        if not modified:
-            continue
-
-        updated = "\n".join(new_lines)
-        conn.execute(
-            sa.text("""
-                UPDATE tool_types
-                SET compose_template = :compose_template
-                WHERE id = :id
-            """),
-            {"compose_template": updated, "id": tool_id},
-        )
-        print(f"Fixed code-server template ({tool_id}): replaced --host with {expected}")
-
-
-def _fix_instance_compose_files(conn) -> None:
-    """Fix existing instance compose files on disk with broken --host override."""
-    from pathlib import Path
-
-    # Use information_schema to check if compose_path column exists
-    col_result = conn.execute(
-        sa.text("""
-            SELECT column_name
-            FROM information_schema.columns
-            WHERE table_name = 'tool_instances'
-            AND column_name = 'compose_path'
-        """)
-    ).fetchone()
-
-    if not col_result:
-        print("compose_path column not found, skipping instance file fixes")
-        return
-
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_path, tool_type_id
-            FROM tool_instances
-            WHERE compose_path IS NOT NULL
-        """)
-    ).fetchall()
-
-    for instance_id, compose_path, tool_type_id in result:
-        path = Path(compose_path)
-        if not path.exists():
-            continue
-
-        try:
-            content = path.read_text()
-        except Exception:
-            continue
-
-        if "--host" not in content:
-            continue
-
-        # Get default_port from tool_type
-        port_result = conn.execute(
-            sa.text("""
-                SELECT default_port FROM tool_types WHERE id = :id
-            """),
-            {"id": tool_type_id},
-        ).fetchone()
-        port = port_result[0] if port_result and port_result[0] else 8443
-        expected = f"--bind-addr 0.0.0.0:{port}"
-
-        try:
-            data = yaml.safe_load(content)
-        except Exception:
-            continue
-
-        if not data or "services" not in data:
-            continue
-
-        modified = False
-        for svc in data["services"].values():
-            if "command" in svc:
-                cmd = svc["command"]
-                if "--host" in cmd:
-                    svc["command"] = expected
-                    modified = True
-
-        if not modified:
-            continue
-
-        try:
-            path.write_text(yaml.dump(data, default_flow_style=False))
-            print(
-                f"Fixed code-server instance compose ({instance_id}): "
-                f"replaced --host with {expected}"
-            )
-        except Exception as exc:
-            print(f"Failed to fix instance {instance_id}: {exc}")
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-    _fix_tool_type_templates(conn)
-    _fix_instance_compose_files(conn)
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/2026_05_29_fix_web_tool_bind_address.py

@@ -1,140 +0,0 @@
-"""fix web tool bind address to 0.0.0.0
-
-Revision ID: 2026_05_29_fix_web_tool_bind_address
-Revises: 2026_05_29_remove_ssh_keys_mount_from_manifest
-Create Date: 2026-05-29 14:00:00.000000
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_fix_web_tool_bind_address"
-down_revision: Union[str, None] = "2026_05_29_remove_ssh_keys_mount_from_manifest"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def _fix_code_server_compose(conn) -> None:
-    """Update code-server compose template to bind to 0.0.0.0."""
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_template, definition_type
-            FROM tool_types
-            WHERE name = 'code-server'
-        """)
-    ).fetchone()
-
-    if result is None:
-        return
-
-    tool_id, compose_template, definition_type = result
-
-    if definition_type != "compose" or not compose_template:
-        return
-
-    # Fix or add command to bind to 0.0.0.0
-    lines = compose_template.split("\n")
-    new_lines = []
-    image_line_idx = -1
-    command_fixed = False
-    for i, line in enumerate(lines):
-        # Replace broken --bind-addr with correct --host
-        if "command:" in line and "--bind-addr" in line:
-            indent = line[: len(line) - len(line.lstrip())]
-            new_lines.append(f"{indent}command: --host 0.0.0.0")
-            command_fixed = True
-            continue
-        new_lines.append(line)
-        if "image:" in line and image_line_idx == -1:
-            image_line_idx = i
-
-    # If no command line exists, insert one after image
-    if not command_fixed and image_line_idx != -1:
-        image_line = lines[image_line_idx]
-        indent = image_line[: len(image_line) - len(image_line.lstrip())]
-        # Insert after the image line in new_lines
-        insert_idx = new_lines.index(image_line) + 1
-        new_lines.insert(insert_idx, f"{indent}command: --host 0.0.0.0")
-        command_fixed = True
-
-    if not command_fixed:
-        return
-
-    updated_compose = "\n".join(new_lines)
-
-    conn.execute(
-        sa.text("""
-            UPDATE tool_types
-            SET compose_template = :compose_template
-            WHERE id = :id
-        """),
-        {"compose_template": updated_compose, "id": tool_id},
-    )
-
-    print(f"Updated code-server tool type ({tool_id}) to bind to 0.0.0.0")
-
-
-def _fix_jupyter_compose(conn) -> None:
-    """Update jupyter-notebook compose template to bind to 0.0.0.0."""
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_template, definition_type
-            FROM tool_types
-            WHERE name = 'jupyter-notebook'
-        """)
-    ).fetchone()
-
-    if result is None:
-        return
-
-    tool_id, compose_template, definition_type = result
-
-    if definition_type != "compose" or not compose_template:
-        return
-
-    if "command:" in compose_template:
-        return
-
-    lines = compose_template.split("\n")
-    new_lines = []
-    image_line_idx = -1
-    for i, line in enumerate(lines):
-        new_lines.append(line)
-        if "image:" in line and image_line_idx == -1:
-            image_line_idx = i
-            indent = line[: len(line) - len(line.lstrip())]
-            # Jupyter needs --ip=0.0.0.0 to bind to all interfaces
-            new_lines.append(
-                f"{indent}command: start-notebook.sh --ip=0.0.0.0 --port=8888 --no-browser"
-            )
-
-    if image_line_idx == -1:
-        return
-
-    updated_compose = "\n".join(new_lines)
-
-    conn.execute(
-        sa.text("""
-            UPDATE tool_types
-            SET compose_template = :compose_template
-            WHERE id = :id
-        """),
-        {"compose_template": updated_compose, "id": tool_id},
-    )
-
-    print(f"Updated jupyter-notebook tool type ({tool_id}) to bind to 0.0.0.0:8888")
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-    _fix_code_server_compose(conn)
-    _fix_jupyter_compose(conn)
-
-
-def downgrade() -> None:
-    # Cannot safely downgrade without knowing the original compose_template
-    pass

apps/api/alembic/versions/2026_05_29_remove_lsio_command_override.py

@@ -1,121 +0,0 @@
-"""Remove broken command override from LSIO code-server templates
-
-Revision ID: 2026_05_29_remove_lsio_command_override
-Revises: 2026_05_29_fix_code_server_bind_addr
-Create Date: 2026-05-29 15:05:00.000000
-
-"""
-
-from collections.abc import Sequence
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_remove_lsio_command_override"
-down_revision: str | None = "2026_05_29_fix_code_server_bind_addr"
-branch_labels: Sequence[str] | None = None
-depends_on: Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-
-    # Fix tool_types templates in DB
-    result = conn.execute(
-        sa.text("""
-            SELECT id, compose_template
-            FROM tool_types
-            WHERE name = 'code-server'
-        """)
-    ).fetchall()
-
-    import yaml
-    from pathlib import Path
-
-    for tool_id, compose_template in result:
-        try:
-            data = yaml.safe_load(compose_template)
-        except Exception:
-            continue
-
-        if not data or "services" not in data:
-            continue
-
-        modified = False
-        for svc in data["services"].values():
-            image = svc.get("image", "")
-            if not image or "linuxserver" not in image:
-                continue
-            if "command" in svc:
-                cmd = svc["command"]
-                if "--bind-addr" in cmd or "--host" in cmd:
-                    del svc["command"]
-                    modified = True
-
-        if modified:
-            updated = yaml.dump(data, default_flow_style=False)
-            conn.execute(
-                sa.text("""
-                    UPDATE tool_types
-                    SET compose_template = :compose_template
-                    WHERE id = :id
-                """),
-                {"compose_template": updated, "id": tool_id},
-            )
-            print(f"Removed broken command override from LSIO template ({tool_id})")
-
-    # Fix existing instance compose files on disk
-    # Use information_schema to check if compose_path column exists
-    col_result = conn.execute(
-        sa.text("""
-            SELECT column_name
-            FROM information_schema.columns
-            WHERE table_name = 'tool_instances'
-            AND column_name = 'compose_path'
-        """)
-    ).fetchone()
-
-    if col_result:
-        result = conn.execute(
-            sa.text("""
-                SELECT id, compose_path
-                FROM tool_instances
-                WHERE compose_path IS NOT NULL
-            """)
-        ).fetchall()
-
-        for instance_id, compose_path in result:
-            path = Path(compose_path)
-            if not path.exists():
-                continue
-            try:
-                content = path.read_text()
-                data = yaml.safe_load(content)
-            except Exception:
-                continue
-
-            if not data or "services" not in data:
-                continue
-
-            modified = False
-            for svc in data["services"].values():
-                image = svc.get("image", "")
-                if not image or "linuxserver" not in image:
-                    continue
-                if "command" in svc:
-                    cmd = svc["command"]
-                    if "--bind-addr" in cmd or "--host" in cmd:
-                        del svc["command"]
-                        modified = True
-
-            if modified:
-                path.write_text(yaml.dump(data, default_flow_style=False))
-                print(
-                    f"Removed broken command override from instance compose "
-                    f"({instance_id})"
-                )
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/2026_05_29_remove_ssh_keys_mount_from_manifest.py

@@ -1,105 +0,0 @@
-"""remove ssh_keys mount from pi-agent manifest
-
-Revision ID: 2026_05_29_remove_ssh_keys_mount_from_manifest
-Revises: 2026_05_29_add_ssh_key_ids_to_tool_instances
-Create Date: 2026-05-29 14:00:00.000000
-
-"""
-
-import json
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_29_remove_ssh_keys_mount_from_manifest"
-down_revision: Union[str, None] = "2026_05_29_add_ssh_key_ids_to_tool_instances"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    """Remove the ssh_keys mount from the pi-agent manifest."""
-    conn = op.get_bind()
-
-    # Get the pi-agent manifest
-    result = conn.execute(
-        sa.text(
-            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
-        )
-    )
-    row = result.fetchone()
-    if not row:
-        return
-
-    manifest_id, manifest_json = row
-    manifest = (
-        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
-    )
-
-    mounts = manifest.get("mounts", [])
-    original_count = len(mounts)
-
-    # Remove any mount named "ssh_keys"
-    filtered_mounts = [m for m in mounts if m.get("name") != "ssh_keys"]
-
-    if len(filtered_mounts) < original_count:
-        manifest["mounts"] = filtered_mounts
-        conn.execute(
-            sa.text(
-                "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
-            ),
-            {
-                "manifest": json.dumps(manifest),
-                "id": manifest_id,
-            },
-        )
-
-
-def downgrade() -> None:
-    """Restore the ssh_keys mount to the pi-agent manifest."""
-    conn = op.get_bind()
-
-    result = conn.execute(
-        sa.text(
-            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
-        )
-    )
-    row = result.fetchone()
-    if not row:
-        return
-
-    manifest_id, manifest_json = row
-    manifest = (
-        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
-    )
-
-    mounts = manifest.get("mounts", [])
-
-    # Check if ssh_keys mount already exists
-    if any(m.get("name") == "ssh_keys" for m in mounts):
-        return
-
-    # Add the ssh_keys mount back
-    mounts.append(
-        {
-            "name": "ssh_keys",
-            "target": "/home/user/.ssh",
-            "source_type": "ssh_key",
-            "mode": "0700",
-            "file_mode": "0600",
-            "readonly": True,
-        }
-    )
-    manifest["mounts"] = mounts
-
-    conn.execute(
-        sa.text(
-            "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
-        ),
-        {
-            "manifest": json.dumps(manifest),
-            "id": manifest_id,
-        },
-    )

apps/api/alembic/versions/2026_06_01_add_workspaces.py

@@ -1,81 +0,0 @@
-"""add workspaces table
-
-Revision ID: 2026_06_01_add_workspaces
-Revises: 2026_05_29_fix_code_server_bind_addr_port
-Create Date: 2026-06-01 10:00:00.000000
-
-"""
-
-from collections.abc import Sequence
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_06_01_add_workspaces"
-down_revision: str | None = "2026_05_29_fix_code_server_bind_addr_port"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def upgrade() -> None:
-    # Create workspaces table
-    op.create_table(
-        "workspaces",
-        sa.Column("id", sa.Uuid(as_uuid=True), primary_key=True),
-        sa.Column("name", sa.String(255), nullable=False),
-        sa.Column(
-            "repo_id",
-            sa.Uuid(as_uuid=True),
-            sa.ForeignKey("git_repositories.id", ondelete="CASCADE"),
-            nullable=False,
-        ),
-        sa.Column(
-            "user_id",
-            sa.Uuid(as_uuid=True),
-            sa.ForeignKey("users.id", ondelete="CASCADE"),
-            nullable=False,
-        ),
-        sa.Column("branch", sa.String(255), nullable=False, server_default="main"),
-        sa.Column("path", sa.String(2048), nullable=False),
-        sa.Column("status", sa.String(16), nullable=False, server_default="ready"),
-        sa.Column("last_sync_at", sa.DateTime(timezone=True), nullable=True),
-        sa.Column(
-            "created_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.text("now()"),
-            nullable=False,
-        ),
-        sa.Column(
-            "updated_at",
-            sa.DateTime(timezone=True),
-            server_default=sa.text("now()"),
-            nullable=False,
-        ),
-        sa.UniqueConstraint("repo_id", "name", name="uq_workspace_repo_name"),
-        if_not_exists=True,
-    )
-
-    op.create_index("idx_workspaces_repo_id", "workspaces", ["repo_id"])
-    op.create_index("idx_workspaces_user_id", "workspaces", ["user_id"])
-    op.create_index("idx_workspaces_status", "workspaces", ["status"])
-
-    # Add workspace_id to tool_instances
-    op.add_column(
-        "tool_instances",
-        sa.Column(
-            "workspace_id",
-            sa.Uuid(as_uuid=True),
-            sa.ForeignKey("workspaces.id", ondelete="SET NULL"),
-            nullable=True,
-        ),
-    )
-    op.create_index(
-        "idx_tool_instances_workspace_id", "tool_instances", ["workspace_id"]
-    )
-
-
-def downgrade() -> None:
-    op.drop_index("idx_tool_instances_workspace_id", table_name="tool_instances")
-    op.drop_column("tool_instances", "workspace_id")
-    op.drop_table("workspaces")

apps/api/alembic/versions/6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py

@@ -1,23 +0,0 @@
-"""merge_remove_is_builtin_and_add_config_profiles
-
-Revision ID: 6fc7bfcf199f
-Revises: 2026_05_23_remove_is_builtin, 2026_05_24_add_config_profiles
-Create Date: 2026-05-24 18:00:43.990361
-"""
-
-
-
-
-# revision identifiers, used by Alembic.
-revision = '6fc7bfcf199f'
-down_revision = ('2026_05_23_remove_is_builtin', '2026_05_24_add_config_profiles')
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/f3d2dc90ba3a_merge_single_interface_and_clone_mode.py

@@ -1,23 +0,0 @@
-"""merge_single_interface_and_clone_mode
-
-Revision ID: f3d2dc90ba3a
-Revises: 0015_single_interface, 2026_05_22_add_clone_mode
-Create Date: 2026-05-24 10:43:14.000000
-
-"""
-from typing import Sequence, Union
-
-
-# revision identifiers, used by Alembic.
-revision: str = "f3d2dc90ba3a"
-down_revision: Union[str, Sequence[str], None] = ("0015_single_interface", "2026_05_22_add_clone_mode")
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

apps/api/src/api/events.py

@@ -1,80 +0,0 @@
-"""SSE streaming endpoint for instance events."""
-
-import asyncio
-import contextlib
-import json
-import uuid
-from collections.abc import AsyncGenerator
-
-from fastapi import APIRouter, Depends, HTTPException, Request, status
-from fastapi.responses import StreamingResponse
-
-from src.auth.dependencies import get_current_user_id
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-
-router = APIRouter(prefix="/events", tags=["events"])
-
-# In-memory connection counter per user (single-process assumption)
-_connection_counts: dict[uuid.UUID, int] = {}
-MAX_CONNECTIONS_PER_USER = 20
-
-
-@router.get("/stream")
-async def events_stream(
-    request: Request,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-) -> StreamingResponse:
-    """Stream instance events via Server-Sent Events.
-
-    Enforces a maximum of 5 concurrent connections per user.
-    """
-    current = _connection_counts.get(user_id, 0)
-    if current >= MAX_CONNECTIONS_PER_USER:
-        raise HTTPException(
-            status_code=status.HTTP_429_TOO_MANY_REQUESTS,
-            detail="Too many SSE connections",
-        )
-
-    _connection_counts[user_id] = current + 1
-
-    async def event_generator() -> AsyncGenerator[str, None]:
-        event_bus = InstanceEventBus()
-        queue: asyncio.Queue[InstanceEventPayload] = asyncio.Queue(maxsize=100)
-
-        async def on_event(payload: InstanceEventPayload) -> None:
-            try:
-                queue.put_nowait(payload)
-            except asyncio.QueueFull:
-                # Drop oldest event to make room
-                with contextlib.suppress(asyncio.QueueEmpty):
-                    queue.get_nowait()
-                with contextlib.suppress(asyncio.QueueFull):
-                    queue.put_nowait(payload)
-
-        unsubscribe = event_bus.subscribe("*", on_event)
-
-        try:
-            while True:
-                try:
-                    payload = await asyncio.wait_for(queue.get(), timeout=30.0)
-                    yield f"event: {payload['event']}\ndata: {json.dumps(payload)}\n\n"
-                except asyncio.TimeoutError:
-                    yield ":ping\n\n"
-        except asyncio.CancelledError:
-            # Client disconnected
-            raise
-        finally:
-            unsubscribe()
-            _connection_counts[user_id] = max(0, _connection_counts.get(user_id, 1) - 1)
-            if _connection_counts[user_id] == 0:
-                _connection_counts.pop(user_id, None)
-
-    return StreamingResponse(
-        event_generator(),
-        media_type="text/event-stream",
-        headers={
-            "Cache-Control": "no-cache",
-            "Connection": "keep-alive",
-            "X-Accel-Buffering": "no",
-        },
-    )

apps/api/src/api/notifications.py

@@ -1,161 +0,0 @@
-"""Notification API endpoints."""
-
-import uuid
-from datetime import datetime
-
-from fastapi import APIRouter, Depends, HTTPException, Query, status
-from pydantic import BaseModel, ConfigDict, Field
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user, get_db_session
-from src.models.user import User
-from src.models.user_config import UserConfig
-from src.services.notification_service import notification_service
-
-router = APIRouter(prefix="/notifications", tags=["notifications"])
-
-
-class NotificationItem(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    user_id: uuid.UUID
-    category: str
-    severity: str
-    title: str
-    message: str | None
-    source_type: str | None
-    source_id: uuid.UUID | None
-    notification_metadata: dict = Field(serialization_alias="metadata")
-    read_at: datetime | None
-    dismissed_at: datetime | None
-    created_at: datetime
-
-
-class NotificationListResponse(BaseModel):
-    items: list[NotificationItem]
-    total: int
-    limit: int
-    offset: int
-
-
-class UnreadCountResponse(BaseModel):
-    count: int
-
-
-class MarkAllReadResponse(BaseModel):
-    marked_count: int
-
-
-class ClearAllResponse(BaseModel):
-    cleared_count: int
-
-
-async def _get_mute_categories(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-) -> list[str]:
-    """Read notification mute categories from user config."""
-    from sqlalchemy import select
-
-    result = await session.execute(
-        select(UserConfig).where(UserConfig.user_id == user_id)
-    )
-    config = result.scalar_one_or_none()
-    if config is None:
-        return []
-    mute_categories = config.config.get("notification_mute_categories", [])
-    if isinstance(mute_categories, list):
-        return mute_categories
-    return []
-
-
-@router.get("", response_model=NotificationListResponse)
-async def list_notifications(
-    limit: int = Query(20, ge=1, le=100),
-    offset: int = Query(0, ge=0),
-    unread_only: bool = Query(False),
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> NotificationListResponse:
-    """List notifications for the authenticated user."""
-    mute_categories = await _get_mute_categories(session, user.id)
-    items, total = await notification_service.list_notifications(
-        session,
-        user.id,
-        limit=limit,
-        offset=offset,
-        unread_only=unread_only,
-        mute_categories=mute_categories,
-    )
-    return NotificationListResponse(
-        items=[NotificationItem.model_validate(item) for item in items],
-        total=total,
-        limit=limit,
-        offset=offset,
-    )
-
-
-@router.get("/unread", response_model=UnreadCountResponse)
-async def get_unread_count(
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> UnreadCountResponse:
-    """Get unread notification count for the authenticated user."""
-    count = await notification_service.get_unread_count(session, user.id)
-    return UnreadCountResponse(count=count)
-
-
-@router.patch("/{notification_id}/read", response_model=NotificationItem)
-async def mark_notification_read(
-    notification_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> NotificationItem:
-    """Mark a single notification as read."""
-    try:
-        notification = await notification_service.mark_read(
-            session, notification_id, user.id
-        )
-    except ValueError as exc:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail="Notification not found",
-        ) from exc
-    return NotificationItem.model_validate(notification)
-
-
-@router.post("/mark-all-read", response_model=MarkAllReadResponse)
-async def mark_all_read(
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> MarkAllReadResponse:
-    """Mark all unread notifications as read."""
-    marked = await notification_service.mark_all_read(session, user.id)
-    return MarkAllReadResponse(marked_count=marked)
-
-
-@router.delete("", status_code=status.HTTP_200_OK)
-async def clear_all_notifications(
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> ClearAllResponse:
-    """Dismiss all notifications for the authenticated user."""
-    cleared = await notification_service.dismiss_all(session, user.id)
-    return ClearAllResponse(cleared_count=cleared)
-
-
-@router.delete("/{notification_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def dismiss_notification(
-    notification_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Soft-delete (dismiss) a single notification."""
-    try:
-        await notification_service.dismiss(session, notification_id, user.id)
-    except ValueError as exc:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail="Notification not found",
-        ) from exc

apps/api/src/api/shared_validators.py

@@ -1,98 +0,0 @@
-"""Shared Pydantic validators for API schemas."""
-
-
-MAX_FOLDER_SIZE_MB = 10
-MAX_FOLDER_SIZE_BYTES = MAX_FOLDER_SIZE_MB * 1024 * 1024
-
-
-def validate_mount_path(v: str | None) -> str | None:
-    """Validate that a mount path is absolute (starts with /).
-
-    Args:
-        v: Mount path string or None.
-
-    Returns:
-        The validated path, or None if input was None.
-
-    Raises:
-        ValueError: If path is not absolute.
-    """
-    if v is None:
-        return v
-    if not v.startswith("/"):
-        raise ValueError("Mount path must be absolute (start with /)")
-    return v
-
-
-def validate_files(v: dict | None, max_size_bytes: int = MAX_FOLDER_SIZE_BYTES) -> dict | None:
-    """Validate file dict for path traversal and size limits.
-
-    Args:
-        v: Dict of {path: content} or None.
-        max_size_bytes: Maximum total size in bytes.
-
-    Returns:
-        The validated dict, or None if input was None.
-
-    Raises:
-        ValueError: If path traversal detected or size limit exceeded.
-    """
-    if v is None:
-        return v
-
-    total_size = 0
-    for path, content in v.items():
-        # Check for path traversal
-        if ".." in path or path.startswith("/"):
-            raise ValueError(f"Invalid file path: {path}")
-        total_size += len(content.encode("utf-8"))
-
-    if total_size > max_size_bytes:
-        raise ValueError(f"Total folder size exceeds {max_size_bytes // (1024 * 1024)}MB limit")
-
-    return v
-
-
-def validate_env_vars(v: dict | None) -> dict | None:
-    """Validate that environment variables is a JSON object.
-
-    Args:
-        v: Dict of env vars or None.
-
-    Returns:
-        The validated dict, or None if input was None.
-
-    Raises:
-        ValueError: If not a dict.
-    """
-    if v is None:
-        return v
-    if not isinstance(v, dict):
-        raise ValueError("environment_variables must be a JSON object")
-    return v
-
-
-def validate_volumes(v: list | None) -> list | None:
-    """Validate volume mounts list.
-
-    Args:
-        v: List of volume dicts or None.
-
-    Returns:
-        The validated list, or None if input was None.
-
-    Raises:
-        ValueError: If not a list or missing required fields.
-    """
-    if v is None:
-        return v
-    if not isinstance(v, list):
-        raise ValueError("volumes must be a JSON array")
-    for i, vol in enumerate(v):
-        if not isinstance(vol, dict):
-            raise ValueError(f"Volume at index {i} must be an object")
-        if "source" not in vol:
-            raise ValueError(f"Volume at index {i} must have 'source' field")
-        if "target" not in vol:
-            raise ValueError(f"Volume at index {i} must have 'target' field")
-    return v

apps/api/src/api/tool_definitions.py

@@ -1,424 +0,0 @@
-"""Tool definition API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, Field
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_definition_manifest import ToolDefinitionManifest
-from src.models.tool_type import ToolType
-from src.services.manifest_compiler import (
-    compile_compose,
-    compile_dockerfile,
-    compile_entrypoint,
-    compute_image_tag,
-    deep_merge,
-    resolve_base,
-)
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/tool-definitions", tags=["tool-definitions"])
-
-
-class CreateToolDefinitionRequest(BaseModel):
-    """Request body for creating a tool definition manifest."""
-
-    model_config = {"extra": "ignore"}
-
-    name: str = Field(description="Unique identifier (kebab-case)")
-    display_name: str = Field(description="Human-readable name")
-    description: str | None = Field(default=None)
-    category: str = Field(default="development")
-    interface_type: str = Field(default="terminal", description="web or terminal")
-    base_image: str | None = Field(default=None, description="Direct base image")
-    base_definition_id: str | None = Field(
-        default=None, description="Reference to a base definition"
-    )
-    base_version: str = Field(default="latest")
-    manifest: dict = Field(description="The full manifest JSON")
-
-
-class UpdateToolDefinitionRequest(BaseModel):
-    """Request body for updating a tool definition manifest."""
-
-    model_config = {"extra": "ignore"}
-
-    display_name: str | None = Field(default=None)
-    description: str | None = Field(default=None)
-    category: str | None = Field(default=None)
-    manifest: dict | None = Field(default=None)
-    base_version: str | None = Field(default=None)
-
-
-@router.post(
-    "",
-    summary="Create tool definition",
-    description="Create a new tool definition manifest.",
-)
-async def create_tool_definition(
-    data: CreateToolDefinitionRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new tool definition manifest.
-
-    Args:
-        data: Manifest data.
-        user_id: Authenticated user ID.
-        session: Database session.
-
-    Returns:
-        Dictionary with created definition details.
-    """
-    # Validate base reference
-    if not data.base_image and not data.base_definition_id:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="Either base_image or base_definition_id is required",
-        )
-
-    base_def_id = None
-    if data.base_definition_id:
-        try:
-            base_def_id = uuid.UUID(data.base_definition_id)
-        except ValueError:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid base_definition_id: {data.base_definition_id}",
-            )
-
-        base_def = await session.get(ToolDefinitionManifest, base_def_id)
-        if not base_def:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Base definition not found: {data.base_definition_id}",
-            )
-        if not base_def.is_base:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Referenced definition is not a base definition",
-            )
-
-    # Check name uniqueness
-    existing = await session.execute(
-        select(ToolDefinitionManifest).where(ToolDefinitionManifest.name == data.name)
-    )
-    if existing.scalar_one_or_none():
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Tool definition '{data.name}' already exists",
-        )
-
-    definition = ToolDefinitionManifest(
-        name=data.name,
-        display_name=data.display_name,
-        description=data.description,
-        category=data.category,
-        interface_type=data.interface_type,
-        base_image=data.base_image,
-        base_definition_id=base_def_id,
-        base_version=data.base_version,
-        manifest=data.manifest,
-        created_by_id=user_id,
-    )
-
-    session.add(definition)
-    await session.commit()
-    await session.refresh(definition)
-
-    logger.info("Created tool definition %s (%s)", definition.id, definition.name)
-
-    return {
-        "id": str(definition.id),
-        "name": definition.name,
-        "display_name": definition.display_name,
-        "description": definition.description,
-        "category": definition.category,
-        "interface_type": definition.interface_type,
-        "base_image": definition.base_image,
-        "base_definition_id": str(definition.base_definition_id)
-        if definition.base_definition_id
-        else None,
-        "base_version": definition.base_version,
-        "manifest": definition.manifest,
-        "is_base": definition.is_base,
-        "created_at": definition.created_at.isoformat(),
-    }
-
-
-@router.get(
-    "",
-    summary="List tool definitions",
-    description="List all tool definition manifests.",
-)
-async def list_tool_definitions(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-    include_bases: bool = True,
-) -> dict:
-    """List all tool definition manifests.
-
-    Args:
-        user_id: Authenticated user ID.
-        session: Database session.
-        include_bases: Whether to include base definitions.
-
-    Returns:
-        Dictionary containing list of definitions.
-    """
-    query = select(ToolDefinitionManifest)
-    if not include_bases:
-        query = query.where(ToolDefinitionManifest.is_base == False)
-
-    result = await session.execute(
-        query.order_by(ToolDefinitionManifest.created_at.desc())
-    )
-    definitions = result.scalars().all()
-
-    return {
-        "definitions": [
-            {
-                "id": str(d.id),
-                "name": d.name,
-                "display_name": d.display_name,
-                "description": d.description,
-                "category": d.category,
-                "interface_type": d.interface_type,
-                "is_base": d.is_base,
-                "base_image": d.base_image,
-                "base_definition_id": str(d.base_definition_id)
-                if d.base_definition_id
-                else None,
-                "base_version": d.base_version,
-                "version": d.version,
-                "created_at": d.created_at.isoformat(),
-            }
-            for d in definitions
-        ]
-    }
-
-
-@router.get(
-    "/{definition_id}",
-    summary="Get tool definition",
-    description="Get a specific tool definition manifest.",
-)
-async def get_tool_definition(
-    definition_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a specific tool definition manifest.
-
-    Args:
-        definition_id: UUID of the definition.
-        user_id: Authenticated user ID.
-        session: Database session.
-
-    Returns:
-        Dictionary with definition details.
-    """
-    definition = await session.get(ToolDefinitionManifest, definition_id)
-    if not definition:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Tool definition not found: {definition_id}",
-        )
-
-    return {
-        "id": str(definition.id),
-        "name": definition.name,
-        "display_name": definition.display_name,
-        "description": definition.description,
-        "category": definition.category,
-        "interface_type": definition.interface_type,
-        "base_image": definition.base_image,
-        "base_definition_id": str(definition.base_definition_id)
-        if definition.base_definition_id
-        else None,
-        "base_version": definition.base_version,
-        "manifest": definition.manifest,
-        "dockerfile_cache": definition.dockerfile_cache,
-        "compose_cache": definition.compose_cache,
-        "version": definition.version,
-        "is_base": definition.is_base,
-        "created_at": definition.created_at.isoformat(),
-        "updated_at": definition.updated_at.isoformat(),
-    }
-
-
-@router.put(
-    "/{definition_id}",
-    summary="Update tool definition",
-    description="Update a tool definition manifest.",
-)
-async def update_tool_definition(
-    definition_id: uuid.UUID,
-    data: UpdateToolDefinitionRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a tool definition manifest.
-
-    Args:
-        definition_id: UUID of the definition.
-        data: Update data.
-        user_id: Authenticated user ID.
-        session: Database session.
-
-    Returns:
-        Dictionary with updated definition details.
-    """
-    definition = await session.get(ToolDefinitionManifest, definition_id)
-    if not definition:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Tool definition not found: {definition_id}",
-        )
-
-    if data.display_name is not None:
-        definition.display_name = data.display_name
-    if data.description is not None:
-        definition.description = data.description
-    if data.category is not None:
-        definition.category = data.category
-    if data.manifest is not None:
-        definition.manifest = data.manifest
-    if data.base_version is not None:
-        definition.base_version = data.base_version
-
-    await session.commit()
-    await session.refresh(definition)
-
-    logger.info("Updated tool definition %s (%s)", definition.id, definition.name)
-
-    return {
-        "id": str(definition.id),
-        "name": definition.name,
-        "display_name": definition.display_name,
-        "manifest": definition.manifest,
-        "updated_at": definition.updated_at.isoformat(),
-    }
-
-
-@router.delete(
-    "/{definition_id}",
-    summary="Delete tool definition",
-    description="Delete a tool definition manifest.",
-)
-async def delete_tool_definition(
-    definition_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Delete a tool definition manifest.
-
-    Args:
-        definition_id: UUID of the definition.
-        user_id: Authenticated user ID.
-        session: Database session.
-
-    Returns:
-        Dictionary with deletion status.
-    """
-    definition = await session.get(ToolDefinitionManifest, definition_id)
-    if not definition:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Tool definition not found: {definition_id}",
-        )
-
-    # Check if any tool types reference this manifest
-    result = await session.execute(
-        select(ToolType).where(ToolType.manifest_id == definition_id)
-    )
-    referencing = result.scalars().all()
-    if referencing:
-        tool_names = ", ".join(t.name for t in referencing)
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Cannot delete: referenced by tool types: {tool_names}",
-        )
-
-    await session.delete(definition)
-    await session.commit()
-
-    logger.info("Deleted tool definition %s (%s)", definition.id, definition.name)
-
-    return {"status": "deleted", "id": str(definition_id)}
-
-
-@router.post(
-    "/{definition_id}/compile",
-    summary="Compile tool definition",
-    description="Compile a manifest to Dockerfile + Compose preview without building.",
-)
-async def compile_tool_definition(
-    definition_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Compile a manifest to Dockerfile + Compose preview.
-
-    Args:
-        definition_id: UUID of the definition.
-        user_id: Authenticated user ID.
-        session: Database session.
-
-    Returns:
-        Dictionary with compiled Dockerfile, Compose, and image tag.
-    """
-    definition = await session.get(ToolDefinitionManifest, definition_id)
-    if not definition:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Tool definition not found: {definition_id}",
-        )
-
-    manifest = dict(definition.manifest)
-
-    # Resolve base if referenced
-    if definition.base_definition_id:
-        base_def = await session.get(
-            ToolDefinitionManifest, definition.base_definition_id
-        )
-        if base_def:
-            base_manifest = dict(base_def.manifest)
-            manifest = resolve_base(deep_merge(base_manifest, manifest))
-
-    # Compile
-    dockerfile = compile_dockerfile(manifest)
-    entrypoint = compile_entrypoint(manifest)
-    image_tag = compute_image_tag(definition.name, manifest)
-
-    # Dummy compose with placeholder variables
-    dummy_vars = {
-        "IMAGE_TAG": image_tag,
-        "INSTANCE_NAME": f"{definition.name}-preview",
-        "INSTANCE_DIR": "/data/instances/preview",
-        "REPO_PATH": "/data/repos/preview",
-        "SSH_PATH": "/data/instances/preview/.ssh",
-        "TOOL_PORT": "8080",
-        "EXTRA_ENV": {},
-        "EXTRA_VOLUMES": [],
-    }
-    compose = compile_compose(manifest, dummy_vars)
-
-    # Update cache
-    definition.dockerfile_cache = dockerfile
-    definition.compose_cache = compose
-    await session.commit()
-
-    return {
-        "id": str(definition.id),
-        "name": definition.name,
-        "dockerfile": dockerfile,
-        "entrypoint": entrypoint,
-        "compose": compose,
-        "image_tag": image_tag,
-    }

apps/api/src/api/tool_types_validation.py

@@ -1,87 +0,0 @@
-"""Shared validation utilities for tool types."""
-
-import re
-
-import yaml
-from fastapi import HTTPException, status
-
-
-def sanitize_template_vars(template: str) -> str:
-    """Replace template variables like {{VAR}} with placeholders to avoid YAML parsing errors."""
-    return re.sub(r"\{\{[A-Za-z_][A-Za-z0-9_]*\}\}", "__PLACEHOLDER__", template)
-
-
-def validate_compose_yaml(template: str) -> dict:
-    """Validate and parse a compose template.
-
-    Args:
-        template: Raw compose template string.
-
-    Returns:
-        Parsed YAML dict.
-
-    Raises:
-        ValueError: If YAML is invalid or missing required keys.
-    """
-    sanitized = sanitize_template_vars(template)
-
-    try:
-        parsed = yaml.safe_load(sanitized)
-    except yaml.YAMLError as e:
-        raise ValueError(f"Invalid YAML: {e}")
-
-    if not isinstance(parsed, dict):
-        raise ValueError("Compose template must be a YAML mapping")
-
-    if "services" not in parsed:
-        raise ValueError("Compose template must contain 'services' key")
-
-    if not parsed["services"]:
-        raise ValueError("Compose template must define at least one service")
-
-    return parsed
-
-
-def check_port_exposed(parsed: dict, port: int) -> bool:
-    """Check if a port is exposed in a parsed compose template.
-
-    Args:
-        parsed: Parsed compose YAML dict.
-        port: Port number to check.
-
-    Returns:
-        True if port is exposed in any service.
-    """
-    port_str = str(port)
-
-    if not isinstance(parsed, dict) or "services" not in parsed:
-        return False
-
-    for service_config in parsed["services"].values():
-        if isinstance(service_config, dict) and "ports" in service_config:
-            for port_mapping in service_config["ports"]:
-                if isinstance(port_mapping, str) and port_str in port_mapping:
-                    return True
-                elif isinstance(port_mapping, int) and port_mapping == port:
-                    return True
-
-    return False
-
-
-def validate_required_variables(template: str, variables: list[str]) -> None:
-    """Validate that all required variables exist in the template.
-
-    Args:
-        template: Compose template string.
-        variables: List of required variable names.
-
-    Raises:
-        HTTPException: If any variable is not found in the template.
-    """
-    for var in variables:
-        placeholder = f"{{{{{var}}}}}"
-        if placeholder not in template:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Required variable '{var}' not found in compose template",
-            )

apps/api/src/api/workspace_files.py

@@ -1,114 +0,0 @@
-"""Workspace file API endpoints."""
-
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
-from src.services.file_service import FileService
-
-router = APIRouter(prefix="/workspaces/{workspace_id}/files")
-
-
-async def _get_workspace(
-    session: AsyncSession,
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID,
-) -> Workspace:
-    from sqlalchemy import select
-
-    result = await session.execute(
-        select(Workspace).where(
-            Workspace.id == workspace_id,
-            Workspace.user_id == user_id,
-        )
-    )
-    workspace = result.scalar_one_or_none()
-    if not workspace:
-        raise HTTPException(status_code=404, detail="Workspace not found")
-    return workspace
-
-
-@router.get("/")
-async def list_files(
-    workspace_id: uuid.UUID,
-    path: str = "",
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List files in a workspace directory."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    service = FileService()
-    try:
-        entries = service.list_directory(workspace, path)
-    except ValueError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-
-    return {
-        "entries": [
-            {
-                "name": e.name,
-                "path": e.path,
-                "type": e.type,
-                "size": e.size,
-            }
-            for e in entries
-        ],
-    }
-
-
-@router.get("/content")
-async def get_file_content(
-    workspace_id: uuid.UUID,
-    path: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get the content of a text file."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    service = FileService()
-    try:
-        content = service.read_file(workspace, path)
-    except FileNotFoundError as exc:
-        raise HTTPException(status_code=404, detail=str(exc)) from exc
-    except ValueError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-
-    return {"content": content, "path": path}
-
-
-@router.post("/content")
-async def write_file(
-    workspace_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Write a file and optionally commit."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    service = FileService()
-
-    file_path = data.get("path", "").strip()
-    content = data.get("content", "")
-    commit_message = data.get("message", "").strip()
-
-    if not file_path:
-        raise HTTPException(status_code=400, detail="File path is required")
-
-    try:
-        service.write_file(workspace, file_path, content)
-    except ValueError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-
-    if commit_message:
-        from src.services.git_operations import GitOperations
-
-        git = GitOperations(workspace)
-        try:
-            await git.commit(commit_message)
-        except RuntimeError as exc:
-            raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {"status": "saved", "path": file_path}

apps/api/src/api/workspace_git.py

@@ -1,203 +0,0 @@
-"""Workspace git API endpoints."""
-
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
-from src.services.git_operations import GitOperations
-
-router = APIRouter(prefix="/workspaces/{workspace_id}/git")
-
-
-async def _get_workspace(
-    session: AsyncSession,
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID,
-) -> Workspace:
-    from sqlalchemy import select
-
-    result = await session.execute(
-        select(Workspace).where(
-            Workspace.id == workspace_id,
-            Workspace.user_id == user_id,
-        )
-    )
-    workspace = result.scalar_one_or_none()
-    if not workspace:
-        raise HTTPException(status_code=404, detail="Workspace not found")
-    return workspace
-
-
-@router.get("/status")
-async def git_status(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get git status for the workspace."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        status = await git.status()
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {
-        "branch": status.branch,
-        "modified": status.modified,
-        "added": status.added,
-        "deleted": status.deleted,
-        "untracked": status.untracked,
-        "ahead": status.ahead,
-        "behind": status.behind,
-    }
-
-
-@router.get("/branches")
-async def git_branches(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List branches for the workspace."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        branches, current = await git.branches()
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {
-        "branches": branches,
-        "current_branch": current,
-    }
-
-
-@router.post("/commit")
-async def git_commit(
-    workspace_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Stage all changes and commit."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    message = data.get("message", "").strip()
-    if not message:
-        raise HTTPException(status_code=400, detail="Commit message is required")
-
-    git = GitOperations(workspace)
-    try:
-        await git.commit(message)
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {"status": "committed"}
-
-
-@router.post("/push")
-async def git_push(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Push current branch."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        await git.push()
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {"status": "pushed"}
-
-
-@router.post("/pull")
-async def git_pull(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Pull current branch."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        await git.pull()
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {"status": "pulled"}
-
-
-@router.post("/fetch")
-async def git_fetch(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Fetch from origin."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        await git.fetch()
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {"status": "fetched"}
-
-
-@router.post("/checkout")
-async def git_checkout(
-    workspace_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Checkout a branch."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    branch = data.get("branch", "").strip()
-    if not branch:
-        raise HTTPException(status_code=400, detail="Branch name is required")
-
-    git = GitOperations(workspace)
-    try:
-        await git.checkout(branch)
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    workspace.branch = branch
-    await session.commit()
-
-    return {"status": "checked_out", "branch": branch}
-
-
-@router.get("/history")
-async def git_history(
-    workspace_id: uuid.UUID,
-    path: str | None = None,
-    limit: int = 50,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get commit history."""
-    workspace = await _get_workspace(session, workspace_id, user_id)
-    git = GitOperations(workspace)
-    try:
-        commits = await git.history(path, limit)
-    except RuntimeError as exc:
-        raise HTTPException(status_code=500, detail=str(exc)) from exc
-
-    return {
-        "commits": [
-            {
-                "hash": c.hash,
-                "message": c.message,
-                "author": c.author,
-                "date": c.date,
-            }
-            for c in commits
-        ],
-    }

apps/api/src/api/workspace_instances.py

@@ -1,60 +0,0 @@
-"""Workspace instance API endpoints."""
-
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.workspace import Workspace
-
-router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
-
-
-async def _get_workspace(
-    session: AsyncSession,
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID,
-) -> Workspace:
-    result = await session.execute(
-        select(Workspace).where(
-            Workspace.id == workspace_id,
-            Workspace.user_id == user_id,
-        )
-    )
-    workspace = result.scalar_one_or_none()
-    if not workspace:
-        raise HTTPException(status_code=404, detail="Workspace not found")
-    return workspace
-
-
-@router.get("/")
-async def list_workspace_instances(
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[dict]:
-    """List tool instances using this workspace."""
-    await _get_workspace(session, workspace_id, user_id)
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.workspace_id == workspace_id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    return [
-        {
-            "id": str(i.id),
-            "name": i.name,
-            "display_name": i.display_name,
-            "status": i.status,
-            "tool_type_id": str(i.tool_type_id),
-            "url": i.url,
-            "port": i.port,
-            "created_at": i.created_at.isoformat() if i.created_at else None,
-        }
-        for i in instances
-    ]

apps/api/src/api/workspaces.py

@@ -1,450 +0,0 @@
-"""Workspace CRUD API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, Query
-from sqlalchemy import func, select
-from sqlalchemy.ext.asyncio import AsyncSession
-from sqlalchemy.orm import selectinload
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
-from src.models.tool_instance import ToolInstance
-from src.models.workspace import Workspace
-from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/projects/{project_id}/repositories/{repo_id}/workspaces")
-all_workspaces_router = APIRouter(prefix="/workspaces")
-
-
-@all_workspaces_router.get("/")
-async def list_all_workspaces(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[dict]:
-    """List all workspaces for the current user across all repos."""
-    instance_count = (
-        select(func.count(ToolInstance.id))
-        .where(ToolInstance.workspace_id == Workspace.id)
-        .correlate(Workspace)
-        .scalar_subquery()
-    )
-
-    result = await session.execute(
-        select(
-            Workspace,
-            GitRepository.name.label("repo_name"),
-            GitRepository.project_id,
-            GitRepository.ssh_key_id.label("repo_ssh_key_id"),
-            instance_count.label("instance_count"),
-        )
-        .join(GitRepository, Workspace.repo_id == GitRepository.id)
-        .where(Workspace.user_id == user_id)
-        .order_by(Workspace.created_at.desc())
-    )
-    rows = result.all()
-
-    return [
-        {
-            "id": str(ws.id),
-            "name": ws.name,
-            "repo_id": str(ws.repo_id),
-            "repo_name": repo_name or "",
-            "repo_ssh_key_id": str(ssh_key_id) if ssh_key_id else None,
-            "project_id": str(project_id) if project_id else "",
-            "project_name": "",
-            "user_id": str(ws.user_id),
-            "branch": ws.branch,
-            "path": ws.path,
-            "status": ws.status,
-            "last_sync_at": ws.last_sync_at.isoformat() if ws.last_sync_at else None,
-            "created_at": ws.created_at.isoformat() if ws.created_at else None,
-            "updated_at": ws.updated_at.isoformat() if ws.updated_at else None,
-            "instance_count": count or 0,
-        }
-        for ws, repo_name, project_id, ssh_key_id, count in rows
-    ]
-
-
-@all_workspaces_router.delete("/{workspace_id}")
-async def delete_workspace_top_level(
-    workspace_id: uuid.UUID,
-    force: bool = Query(False),
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Delete a workspace via top-level path."""
-    workspace = await session.get(Workspace, workspace_id)
-    if not workspace or workspace.user_id != user_id:
-        raise HTTPException(status_code=404, detail="Workspace not found")
-
-    manager = WorkspaceManager()
-    try:
-        await manager.delete(workspace, force=force, session=session)
-        await session.commit()
-    except WorkspaceHasInstancesError as exc:
-        await session.rollback()
-        raise HTTPException(
-            status_code=409,
-            detail={
-                "message": "Workspace has running tool instances",
-                "instances": exc.instances,
-            },
-        ) from exc
-    except Exception as exc:
-        await session.rollback()
-        logger.error("Failed to delete workspace: %s", exc)
-        raise HTTPException(
-            status_code=500, detail="Failed to delete workspace"
-        ) from exc
-
-    return {"status": "deleted"}
-
-
-@all_workspaces_router.post("/")
-async def create_workspace_top_level(
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a workspace directly (no nested project/repo path)."""
-    repo_id_str = data.get("repo_id", "").strip()
-    if not repo_id_str:
-        raise HTTPException(status_code=400, detail="repo_id is required")
-
-    try:
-        repo_id = uuid.UUID(repo_id_str)
-    except ValueError as exc:
-        raise HTTPException(status_code=400, detail="Invalid repo_id format") from exc
-
-    repo = await session.get(GitRepository, repo_id)
-    if not repo or repo.owner_id != user_id:
-        raise HTTPException(status_code=404, detail="Repository not found")
-
-    name = data.get("name", "").strip()
-    branch = data.get("branch", "main").strip()
-
-    if not name:
-        raise HTTPException(status_code=400, detail="Workspace name is required")
-
-    manager = WorkspaceManager()
-    try:
-        workspace = await manager.create(repo, user_id, name, branch, session=session)
-        session.add(workspace)
-        await session.commit()
-    except Exception as exc:
-        await session.rollback()
-        logger.error("Failed to create workspace: %s", exc)
-        raise HTTPException(
-            status_code=409,
-            detail="Workspace name already exists for this repository",
-        ) from exc
-
-    await session.refresh(workspace)
-    return {
-        "id": str(workspace.id),
-        "name": workspace.name,
-        "repo_id": str(workspace.repo_id),
-        "branch": workspace.branch,
-        "path": workspace.path,
-        "status": workspace.status,
-        "created_at": workspace.created_at.isoformat()
-        if workspace.created_at
-        else None,
-    }
-
-
-@router.get("/")
-async def list_workspaces(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[dict]:
-    """List workspaces for a repository, with instance counts."""
-    # Verify repo belongs to project and user
-    repo = await _get_repo(session, repo_id, project_id, user_id)
-
-    # Build subquery for instance counts
-    instance_count = (
-        select(func.count(ToolInstance.id))
-        .where(ToolInstance.workspace_id == Workspace.id)
-        .correlate(Workspace)
-        .scalar_subquery()
-    )
-
-    result = await session.execute(
-        select(
-            Workspace,
-            instance_count.label("instance_count"),
-        )
-        .where(Workspace.repo_id == repo_id)
-        .order_by(Workspace.created_at.desc())
-    )
-    rows = result.all()
-
-    return [
-        {
-            "id": str(ws.id),
-            "name": ws.name,
-            "repo_id": str(ws.repo_id),
-            "repo_name": repo.name,
-            "repo_ssh_key_id": str(repo.ssh_key_id) if repo.ssh_key_id else None,
-            "project_id": str(repo.project_id) if repo.project_id else "",
-            "project_name": repo.project.name if repo.project else "",
-            "user_id": str(ws.user_id),
-            "branch": ws.branch,
-            "path": ws.path,
-            "status": ws.status,
-            "last_sync_at": ws.last_sync_at.isoformat() if ws.last_sync_at else None,
-            "created_at": ws.created_at.isoformat() if ws.created_at else None,
-            "updated_at": ws.updated_at.isoformat() if ws.updated_at else None,
-            "instance_count": count or 0,
-        }
-        for ws, count in rows
-    ]
-
-
-@router.post("/")
-async def create_workspace(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new workspace by cloning a repository branch."""
-    repo = await _get_repo(session, repo_id, project_id, user_id)
-
-    name = data.get("name", "").strip()
-    branch = data.get("branch", "main").strip()
-
-    if not name:
-        raise HTTPException(status_code=400, detail="Workspace name is required")
-    if not branch:
-        raise HTTPException(status_code=400, detail="Branch is required")
-
-    manager = WorkspaceManager()
-    try:
-        workspace = await manager.create(repo, user_id, name, branch, session=session)
-        session.add(workspace)
-        await session.commit()
-    except HTTPException:
-        raise
-    except ValueError as exc:
-        await session.rollback()
-        logger.error("Failed to create workspace: %s", exc)
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-    except Exception as exc:
-        await session.rollback()
-        logger.error("Failed to create workspace: %s", exc)
-        raise HTTPException(
-            status_code=409,
-            detail="Workspace name already exists for this repository",
-        ) from exc
-
-    await session.refresh(workspace)
-    return {
-        "id": str(workspace.id),
-        "name": workspace.name,
-        "repo_id": str(workspace.repo_id),
-        "branch": workspace.branch,
-        "path": workspace.path,
-        "status": workspace.status,
-        "created_at": workspace.created_at.isoformat()
-        if workspace.created_at
-        else None,
-    }
-
-
-@router.get("/{workspace_id}")
-async def get_workspace_detail(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get workspace details."""
-    repo = await _get_repo(session, repo_id, project_id, user_id)
-    workspace = await _get_workspace(session, workspace_id, repo_id)
-
-    # Count instances
-    result = await session.execute(
-        select(func.count(ToolInstance.id)).where(
-            ToolInstance.workspace_id == workspace_id
-        )
-    )
-    instance_count = result.scalar() or 0
-
-    return {
-        "id": str(workspace.id),
-        "name": workspace.name,
-        "repo_id": str(workspace.repo_id),
-        "repo_name": repo.name,
-        "user_id": str(workspace.user_id),
-        "branch": workspace.branch,
-        "path": workspace.path,
-        "status": workspace.status,
-        "last_sync_at": workspace.last_sync_at.isoformat()
-        if workspace.last_sync_at
-        else None,
-        "created_at": workspace.created_at.isoformat()
-        if workspace.created_at
-        else None,
-        "updated_at": workspace.updated_at.isoformat()
-        if workspace.updated_at
-        else None,
-        "instance_count": instance_count,
-    }
-
-
-@router.patch("/{workspace_id}")
-async def update_workspace(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    workspace_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update workspace name or branch."""
-    await _get_repo(session, repo_id, project_id, user_id)
-    workspace = await _get_workspace(session, workspace_id, repo_id)
-
-    new_name = data.get("name", "").strip()
-    new_branch = data.get("branch", "").strip()
-
-    if new_name:
-        workspace.name = new_name
-    if new_branch:
-        workspace.branch = new_branch
-
-    try:
-        await session.commit()
-    except Exception as exc:
-        await session.rollback()
-        logger.error("Failed to update workspace: %s", exc)
-        raise HTTPException(
-            status_code=409,
-            detail="Workspace name already exists for this repository",
-        ) from exc
-
-    return {
-        "id": str(workspace.id),
-        "name": workspace.name,
-        "branch": workspace.branch,
-        "status": workspace.status,
-    }
-
-
-@router.delete("/{workspace_id}")
-async def delete_workspace(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    workspace_id: uuid.UUID,
-    force: bool = Query(False),
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Delete a workspace. Returns 409 if instances exist and force=False."""
-    await _get_repo(session, repo_id, project_id, user_id)
-    workspace = await _get_workspace(session, workspace_id, repo_id)
-
-    manager = WorkspaceManager()
-    try:
-        await manager.delete(workspace, force=force, session=session)
-        await session.commit()
-    except WorkspaceHasInstancesError as exc:
-        await session.rollback()
-        raise HTTPException(
-            status_code=409,
-            detail={
-                "message": "Workspace has running tool instances",
-                "instances": exc.instances,
-            },
-        ) from exc
-    except Exception as exc:
-        await session.rollback()
-        logger.error("Failed to delete workspace: %s", exc)
-        raise HTTPException(
-            status_code=500, detail="Failed to delete workspace"
-        ) from exc
-
-    return {"status": "deleted"}
-
-
-@router.post("/{workspace_id}/sync")
-async def sync_workspace(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    workspace_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Sync workspace with remote. Returns 409 if branch was deleted."""
-    await _get_repo(session, repo_id, project_id, user_id)
-    workspace = await _get_workspace(session, workspace_id, repo_id)
-
-    manager = WorkspaceManager()
-    result = await manager.sync(workspace, session=session)
-
-    if result.branch_deleted:
-        raise HTTPException(
-            status_code=409,
-            detail={
-                "message": f"Branch '{workspace.branch}' was deleted from remote",
-                "branch_deleted": True,
-            },
-        )
-
-    await session.commit()
-    return {
-        "branch_deleted": False,
-        "pulled": True,
-        "last_sync_at": workspace.last_sync_at.isoformat()
-        if workspace.last_sync_at
-        else None,
-    }
-
-
-async def _get_repo(
-    session: AsyncSession,
-    repo_id: uuid.UUID,
-    project_id: uuid.UUID,
-    user_id: uuid.UUID,
-) -> GitRepository:
-    """Fetch and validate repository access."""
-    result = await session.execute(
-        select(GitRepository)
-        .where(
-            GitRepository.id == repo_id,
-            GitRepository.project_id == project_id,
-        )
-        .options(selectinload(GitRepository.project))
-    )
-    repo = result.scalar_one_or_none()
-    if not repo:
-        raise HTTPException(status_code=404, detail="Repository not found")
-    return repo
-
-
-async def _get_workspace(
-    session: AsyncSession,
-    workspace_id: uuid.UUID,
-    repo_id: uuid.UUID,
-) -> Workspace:
-    """Fetch and validate workspace."""
-    result = await session.execute(
-        select(Workspace).where(
-            Workspace.id == workspace_id,
-            Workspace.repo_id == repo_id,
-        )
-    )
-    workspace = result.scalar_one_or_none()
-    if not workspace:
-        raise HTTPException(status_code=404, detail="Workspace not found")
-    return workspace

apps/api/src/models/health_check.py

@@ -1,30 +0,0 @@
-"""SQLAlchemy model for health check snapshots."""
-
-import uuid
-from datetime import datetime
-
-from sqlalchemy import Boolean, DateTime, ForeignKey, Integer, String, Text, Uuid, func
-from sqlalchemy.orm import Mapped, mapped_column
-
-from src.models.base import Base, UUIDPrimaryKeyMixin
-
-
-class HealthCheck(UUIDPrimaryKeyMixin, Base):
-    __tablename__ = "health_checks"
-
-    instance_id: Mapped[uuid.UUID] = mapped_column(
-        Uuid(as_uuid=True),
-        ForeignKey("tool_instances.id", ondelete="CASCADE"),
-        nullable=False,
-    )
-    container_status: Mapped[str | None] = mapped_column(String(50), nullable=True)
-    container_healthy: Mapped[bool | None] = mapped_column(Boolean, nullable=True)
-    tunnel_healthy: Mapped[bool | None] = mapped_column(Boolean, nullable=True)
-    exit_code: Mapped[int | None] = mapped_column(Integer, nullable=True)
-    probe_status: Mapped[str | None] = mapped_column(String(50), nullable=True)
-    probe_output: Mapped[str | None] = mapped_column(Text, nullable=True)
-    checked_at: Mapped[datetime] = mapped_column(
-        DateTime(timezone=True),
-        server_default=func.now(),
-        nullable=False,
-    )

apps/api/src/models/instance_event.py

@@ -1,39 +0,0 @@
-"""SQLAlchemy model for instance lifecycle event audit rows."""
-
-import uuid
-from datetime import datetime
-from typing import Any
-
-from sqlalchemy import DateTime, ForeignKey, JSON, String, Text, Uuid, func
-from sqlalchemy.orm import Mapped, mapped_column
-
-from src.models.base import Base, UUIDPrimaryKeyMixin
-
-
-class InstanceEvent(UUIDPrimaryKeyMixin, Base):
-    __tablename__ = "instance_events"
-
-    instance_id: Mapped[uuid.UUID] = mapped_column(
-        Uuid(as_uuid=True),
-        ForeignKey("tool_instances.id", ondelete="CASCADE"),
-        nullable=False,
-    )
-    event_type: Mapped[str] = mapped_column(String(50), nullable=False)
-    status: Mapped[str | None] = mapped_column(String(50), nullable=True)
-    message: Mapped[str | None] = mapped_column(Text, nullable=True)
-    created_by: Mapped[uuid.UUID | None] = mapped_column(
-        Uuid(as_uuid=True),
-        ForeignKey("users.id", ondelete="SET NULL"),
-        nullable=True,
-    )
-    event_metadata: Mapped[dict[str, Any]] = mapped_column(
-        "metadata",
-        JSON,
-        nullable=False,
-        default=dict,
-    )
-    created_at: Mapped[datetime] = mapped_column(
-        DateTime(timezone=True),
-        server_default=func.now(),
-        nullable=False,
-    )

apps/api/src/models/notification.py

@@ -1,43 +0,0 @@
-"""Notification SQLAlchemy model."""
-
-from datetime import datetime
-from typing import Any
-import uuid
-
-from sqlalchemy import DateTime, ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column
-from sqlalchemy.sql import func
-
-from src.models.base import Base, UUIDPrimaryKeyMixin
-
-
-class Notification(UUIDPrimaryKeyMixin, Base):
-    __tablename__ = "notifications"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(as_uuid=True),
-        ForeignKey("users.id", ondelete="CASCADE"),
-        nullable=False,
-        index=True,
-    )
-    category: Mapped[str] = mapped_column(String(32), nullable=False)
-    severity: Mapped[str] = mapped_column(String(16), nullable=False)
-    title: Mapped[str] = mapped_column(String(255), nullable=False)
-    message: Mapped[str | None] = mapped_column(Text, nullable=True)
-    source_type: Mapped[str | None] = mapped_column(String(64), nullable=True)
-    source_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(as_uuid=True), nullable=True
-    )
-    notification_metadata: Mapped[dict[str, Any]] = mapped_column(
-        "metadata", JSON, nullable=False, default=dict
-    )
-    read_at: Mapped[datetime | None] = mapped_column(
-        DateTime(timezone=True), nullable=True, index=True
-    )
-    dismissed_at: Mapped[datetime | None] = mapped_column(
-        DateTime(timezone=True), nullable=True
-    )
-    created_at: Mapped[datetime] = mapped_column(
-        DateTime(timezone=True), server_default=func.now(), nullable=False, index=True
-    )

apps/api/src/models/terminal_session.py

@@ -1,37 +0,0 @@
-"""Terminal session database model."""
-
-import uuid
-from datetime import datetime
-
-from sqlalchemy import DateTime, ForeignKey, String
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-
-class TerminalSessionModel(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    """Database model for terminal session metadata."""
-
-    __tablename__ = "terminal_sessions"
-
-    instance_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(),
-        ForeignKey("tool_instances.id", ondelete="CASCADE"),
-        nullable=False,
-        index=True,
-    )
-    name: Mapped[str | None] = mapped_column(String(255), nullable=True)
-    status: Mapped[str] = mapped_column(
-        String(50),
-        nullable=False,
-        default="active",
-    )
-    last_activity_at: Mapped[datetime | None] = mapped_column(
-        DateTime(timezone=True),
-        nullable=True,
-    )
-    closed_at: Mapped[datetime | None] = mapped_column(
-        DateTime(timezone=True),
-        nullable=True,
-    )

apps/api/src/models/tool_definition_manifest.py

@@ -1,67 +0,0 @@
-"""Tool Definition Manifest model."""
-
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class ToolDefinitionManifest(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    """A declarative manifest that compiles to Dockerfile + Compose.
-
-    Can be either:
-    - A base definition (is_base=True) with a FROM image and common packages
-    - A tool definition (is_base=False) that references a base + adds specifics
-    """
-
-    __tablename__ = "tool_definition_manifests"
-
-    name: Mapped[str] = mapped_column(String(64), unique=True, nullable=False)
-    display_name: Mapped[str] = mapped_column(String(128), nullable=False)
-    description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    category: Mapped[str | None] = mapped_column(String(64), nullable=True)
-    interface_type: Mapped[str] = mapped_column(String(16), nullable=False)
-
-    # Base: either a direct image or a reference to another manifest
-    base_image: Mapped[str | None] = mapped_column(String(256), nullable=True)
-    base_definition_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(),
-        ForeignKey("tool_definition_manifests.id"),
-        nullable=True,
-    )
-    base_version: Mapped[str] = mapped_column(
-        String(32), nullable=False, default="latest"
-    )
-
-    # The full manifest JSON
-    manifest: Mapped[dict] = mapped_column(JSON, nullable=False)
-
-    # Caches for quick inspection
-    dockerfile_cache: Mapped[str | None] = mapped_column(Text, nullable=True)
-    compose_cache: Mapped[str | None] = mapped_column(Text, nullable=True)
-
-    # Versioning
-    version: Mapped[str] = mapped_column(String(32), nullable=False, default="v1")
-    is_base: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
-
-    created_by_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(),
-        ForeignKey("users.id"),
-        nullable=True,
-    )
-
-    # Relationships
-    created_by: Mapped["User | None"] = relationship(
-        foreign_keys=[created_by_id],
-    )
-    base_definition: Mapped["ToolDefinitionManifest | None"] = relationship(
-        remote_side="ToolDefinitionManifest.id",
-        foreign_keys=[base_definition_id],
-    )

apps/api/src/models/workspace.py

@@ -1,50 +0,0 @@
-"""Workspace model for persistent writable repo clones."""
-
-from __future__ import annotations
-
-import uuid
-from datetime import datetime
-from typing import TYPE_CHECKING
-
-from sqlalchemy import DateTime, ForeignKey, String, UniqueConstraint
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin
-
-if TYPE_CHECKING:
-    from src.models.git_repository import GitRepository
-    from src.models.user import User
-
-
-class Workspace(Base, TimestampMixin):
-    """A persistent, writable local clone of a Git repository.
-
-    Users create workspaces explicitly, then start tool instances on them.
-    Multiple tool instances can share the same workspace.
-    """
-
-    __tablename__ = "workspaces"
-
-    id: Mapped[uuid.UUID] = mapped_column(primary_key=True, default=uuid.uuid4)
-    name: Mapped[str] = mapped_column(String(255), nullable=False)
-    repo_id: Mapped[uuid.UUID] = mapped_column(
-        ForeignKey("git_repositories.id", ondelete="CASCADE"),
-        nullable=False,
-    )
-    user_id: Mapped[uuid.UUID] = mapped_column(
-        ForeignKey("users.id", ondelete="CASCADE"),
-        nullable=False,
-    )
-    branch: Mapped[str] = mapped_column(String(255), nullable=False, default="main")
-    path: Mapped[str] = mapped_column(String(2048), nullable=False)
-    status: Mapped[str] = mapped_column(String(16), nullable=False, default="ready")
-    last_sync_at: Mapped[datetime | None] = mapped_column(
-        DateTime(timezone=True), nullable=True
-    )
-
-    __table_args__ = (
-        UniqueConstraint("repo_id", "name", name="uq_workspace_repo_name"),
-    )
-
-    repository: Mapped[GitRepository] = relationship("GitRepository")
-    owner: Mapped[User] = relationship("User")

apps/api/src/services/clone.py

@@ -1,97 +0,0 @@
-"""Clone service for repository cloning and dirty state checking."""
-
-import logging
-import os
-import subprocess
-from pathlib import Path
-
-logger = logging.getLogger(__name__)
-
-
-def clone_repository(
-    remote_url: str,
-    ssh_key_path: str | None,
-    instance_dir: str,
-    branch: str = "main",
-) -> str:
-    """Clone a git repository into the instance directory.
-
-    Args:
-        remote_url: Git remote URL (SSH or HTTPS)
-        ssh_key_path: Path to SSH private key for authentication (optional)
-        instance_dir: Path to instance directory
-        branch: Branch to clone (default: main)
-
-    Returns:
-        Path to the cloned repository
-    """
-    clone_path = Path(instance_dir) / "repo-clone"
-    clone_path.mkdir(parents=True, exist_ok=True)
-
-    env = os.environ.copy()
-    if ssh_key_path:
-        # Use SSH key for cloning
-        env["GIT_SSH_COMMAND"] = f"ssh -i {ssh_key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
-
-    cmd = [
-        "git",
-        "clone",
-        "--branch", branch,
-        "--single-branch",
-        remote_url,
-        str(clone_path),
-    ]
-
-    logger.debug("Cloning repository %s (branch: %s) into %s", remote_url, branch, clone_path)
-    result = subprocess.run(
-        cmd,
-        capture_output=True,
-        text=True,
-        env=env,
-        timeout=300,
-    )
-
-    if result.returncode != 0:
-        logger.error("Git clone failed: %s", result.stderr)
-        raise RuntimeError(f"Failed to clone repository: {result.stderr}")
-
-    logger.debug("Successfully cloned repository into %s", clone_path)
-    return str(clone_path)
-
-
-def check_dirty_state(clone_path: str) -> tuple[bool, list[str]]:
-    """Check for uncommitted changes in a cloned repository.
-
-    Args:
-        clone_path: Path to the cloned repository
-
-    Returns:
-        Tuple of (is_dirty, list_of_changed_files)
-    """
-    result = subprocess.run(
-        ["git", "-C", clone_path, "status", "--short"],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode != 0:
-        logger.warning("Failed to check git status: %s", result.stderr)
-        return False, []
-
-    changed_files = [line.strip() for line in result.stdout.split("\n") if line.strip()]
-    is_dirty = len(changed_files) > 0
-
-    return is_dirty, changed_files
-
-
-def remove_clone_directory(instance_dir: str) -> None:
-    """Remove the cloned repository from the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-    """
-    clone_path = Path(instance_dir) / "repo-clone"
-    if clone_path.exists():
-        import shutil
-        shutil.rmtree(clone_path)
-        logger.debug("Removed clone directory: %s", clone_path)

apps/api/src/services/config_profile_resolver.py

@@ -1,567 +0,0 @@
-"""Config profile resolver service.
-
-Provides recursive ordered include resolution with deterministic merge rules
-and cycle protection.
-"""
-
-import logging
-import os
-import uuid
-from dataclasses import dataclass, field
-from typing import Any
-
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
-
-logger = logging.getLogger(__name__)
-
-
-class ConfigProfileCycleError(Exception):
-    """Raised when a cycle is detected in profile includes."""
-
-    pass
-
-
-class ConfigProfileNotFoundError(Exception):
-    """Raised when a referenced profile is not found."""
-
-    pass
-
-
-@dataclass
-class ResolvedMount:
-    """A resolved mount with merged files and final mode."""
-
-    target: str
-    mode: str
-    files: dict[str, str] = field(default_factory=dict)
-    overridden_files: dict[str, str] = field(default_factory=dict)
-
-
-@dataclass
-class ResolvedProfile:
-    """The fully resolved output of a config profile."""
-
-    profile_id: uuid.UUID
-    profile_name: str
-    env_vars: dict[str, str] = field(default_factory=dict)
-    runtime_hints: dict[str, Any] = field(default_factory=dict)
-    mounts: dict[str, ResolvedMount] = field(default_factory=dict)
-    git_mounts: list[dict[str, Any]] = field(default_factory=list)
-    files: dict[str, str] = field(default_factory=dict)
-    env_overrides: dict[str, str] = field(default_factory=dict)
-    hint_overrides: dict[str, str] = field(default_factory=dict)
-    file_overrides: dict[str, str] = field(default_factory=dict)
-    mount_overrides: dict[str, str] = field(default_factory=dict)
-    included_profiles: list[dict[str, Any]] = field(default_factory=list)
-
-
-def _detect_cycle(
-    profile_id: uuid.UUID, visited: set[uuid.UUID], path: list[uuid.UUID]
-) -> bool:
-    """Detect if adding profile_id to path would create a cycle.
-
-    Args:
-        profile_id: The profile ID to check.
-        visited: Set of already-visited profile IDs in current resolution.
-        path: Current resolution path for error reporting.
-
-    Returns:
-        True if a cycle would be created.
-    """
-    if profile_id in visited:
-        return True
-    return False
-
-
-def _merge_env_vars(
-    base: dict[str, str],
-    overlay: dict[str, str],
-    overrides: dict[str, str],
-    source_name: str,
-) -> dict[str, str]:
-    """Merge env vars, tracking overrides.
-
-    Later values replace earlier values.
-    """
-    result = dict(base)
-    for key, value in overlay.items():
-        if key in result and result[key] != value:
-            overrides[key] = source_name
-        result[key] = value
-    return result
-
-
-def _merge_runtime_hints(
-    base: dict[str, Any],
-    overlay: dict[str, Any],
-    overrides: dict[str, str],
-    source_name: str,
-) -> dict[str, Any]:
-    """Merge runtime hints, tracking overrides.
-
-    Later values replace earlier values.
-    """
-    result = dict(base)
-    for key, value in overlay.items():
-        if key in result and result[key] != value:
-            overrides[key] = source_name
-        result[key] = value
-    return result
-
-
-def _merge_files(
-    base: dict[str, str],
-    overlay: dict[str, str],
-    overrides: dict[str, str],
-    source_name: str,
-) -> dict[str, str]:
-    """Merge file maps, tracking overrides.
-
-    Later relative file paths win.
-    """
-    result = dict(base)
-    for path, content in overlay.items():
-        if path in result and result[path] != content:
-            overrides[path] = source_name
-        result[path] = content
-    return result
-
-
-def _merge_mounts(
-    base: dict[str, ResolvedMount],
-    overlay: list[dict[str, Any]],
-    overrides: dict[str, str],
-    source_name: str,
-) -> dict[str, ResolvedMount]:
-    """Merge mounts, tracking overrides.
-
-    Mounts with the same target path have their file maps merged and later
-    relative file paths win. Mode conflicts: later layer wins.
-    """
-    result = dict(base)
-    for mount_data in overlay:
-        target = mount_data["target"]
-        mode = mount_data.get("mode", "rw")
-        files = mount_data.get("files", {})
-
-        if target in result:
-            existing = result[target]
-            merged_files = dict(existing.files)
-            file_overrides = dict(existing.overridden_files)
-            for rel_path, content in files.items():
-                if rel_path in merged_files and merged_files[rel_path] != content:
-                    file_overrides[rel_path] = source_name
-                merged_files[rel_path] = content
-            if existing.mode != mode:
-                overrides[target] = source_name
-            result[target] = ResolvedMount(
-                target=target,
-                mode=mode,
-                files=merged_files,
-                overridden_files=file_overrides,
-            )
-        else:
-            result[target] = ResolvedMount(
-                target=target,
-                mode=mode,
-                files=dict(files),
-            )
-    return result
-
-
-def _merge_git_mounts(
-    base: list[dict[str, Any]],
-    overlay: list[dict[str, Any]],
-    source_name: str,
-) -> list[dict[str, Any]]:
-    """Merge git mounts from included profiles.
-
-    Entries with the same remote_url + branch have their mappings concatenated.
-    Different repos are kept as separate entries.
-    All entries are normalized to the mappings format.
-    """
-    result = list(base)
-    # Normalize existing entries to mappings format
-    for i, m in enumerate(result):
-        result[i] = _normalize_git_mount_entry(dict(m))
-
-    # Build lookup by (remote_url, branch)
-    seen = {}
-    for i, m in enumerate(result):
-        key = (m["remote_url"], m.get("branch"))
-        seen[key] = i
-
-    for mount in overlay:
-        mount = _normalize_git_mount_entry(dict(mount))
-        key = (mount["remote_url"], mount.get("branch"))
-        if key in seen:
-            # Same repo+branch: concatenate mappings, dedup by (source_path, target_path)
-            existing = result[seen[key]]
-            existing_sources = {
-                (m["source_path"], m["target_path"])
-                for m in existing.get("mappings", [])
-            }
-            for mapping in mount.get("mappings", []):
-                map_key = (mapping["source_path"], mapping["target_path"])
-                if map_key not in existing_sources:
-                    existing["mappings"].append(dict(mapping))
-                    existing_sources.add(map_key)
-        else:
-            seen[key] = len(result)
-            result.append(mount)
-    return result
-
-
-def _normalize_git_mount_entry(entry: dict[str, Any]) -> dict[str, Any]:
-    """Normalize a git mount entry to the unified mappings format.
-
-    Converts legacy source_path + target_path into a single-entry mappings array.
-    """
-    entry = dict(entry)
-    if "mappings" not in entry or not entry.get("mappings"):
-        source = entry.get("source_path", ".")
-        target = entry.get("target_path")
-        if target is not None:
-            entry["mappings"] = [{"source_path": source, "target_path": target}]
-    # Remove legacy fields once normalized
-    entry.pop("source_path", None)
-    entry.pop("target_path", None)
-    return entry
-
-
-async def _resolve_profile_recursive(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    visited: set[uuid.UUID],
-    path: list[uuid.UUID],
-) -> ResolvedProfile:
-    """Recursively resolve a profile and its includes.
-
-    Args:
-        session: Database session.
-        profile_id: Profile ID to resolve.
-        visited: Set of already-visited profile IDs in current resolution chain.
-        path: Current resolution path for error reporting.
-
-    Returns:
-        ResolvedProfile with all includes merged.
-
-    Raises:
-        ConfigProfileCycleError: If a cycle is detected.
-        ConfigProfileNotFoundError: If the profile is not found.
-    """
-    if _detect_cycle(profile_id, visited, path):
-        cycle_path = " -> ".join(str(p) for p in path + [profile_id])
-        raise ConfigProfileCycleError(
-            f"Cycle detected in profile includes: {cycle_path}"
-        )
-
-    profile = await session.get(ConfigProfile, profile_id)
-    if profile is None:
-        raise ConfigProfileNotFoundError(f"Config profile not found: {profile_id}")
-
-    new_visited = visited | {profile_id}
-    new_path = path + [profile_id]
-
-    result = ResolvedProfile(
-        profile_id=profile.id,
-        profile_name=profile.name,
-    )
-
-    # Resolve includes in order
-    include_query = (
-        select(ConfigProfileInclude)
-        .where(ConfigProfileInclude.profile_id == profile_id)
-        .order_by(ConfigProfileInclude.order_index)
-    )
-    include_result = await session.execute(include_query)
-    includes = include_result.scalars().all()
-
-    for include in includes:
-        included = await _resolve_profile_recursive(
-            session, include.included_profile_id, new_visited, new_path
-        )
-        result.included_profiles.append(
-            {
-                "id": str(included.profile_id),
-                "name": included.profile_name,
-            }
-        )
-
-        result.env_vars = _merge_env_vars(
-            result.env_vars,
-            included.env_vars,
-            result.env_overrides,
-            included.profile_name,
-        )
-        result.runtime_hints = _merge_runtime_hints(
-            result.runtime_hints,
-            included.runtime_hints,
-            result.hint_overrides,
-            included.profile_name,
-        )
-        result.files = _merge_files(
-            result.files, included.files, result.file_overrides, included.profile_name
-        )
-        result.mounts = _merge_mounts(
-            result.mounts,
-            [
-                {"target": m.target, "mode": m.mode, "files": m.files}
-                for m in included.mounts.values()
-            ],
-            result.mount_overrides,
-            included.profile_name,
-        )
-        result.git_mounts = _merge_git_mounts(
-            result.git_mounts, included.git_mounts, included.profile_name
-        )
-
-    # Apply the profile's own settings (selected profile overrides includes)
-    result.env_vars = _merge_env_vars(
-        result.env_vars,
-        profile.env_vars or {},
-        result.env_overrides,
-        profile.name,
-    )
-    result.runtime_hints = _merge_runtime_hints(
-        result.runtime_hints,
-        profile.runtime_hints or {},
-        result.hint_overrides,
-        profile.name,
-    )
-    result.files = _merge_files(
-        result.files,
-        profile.files or {},
-        result.file_overrides,
-        profile.name,
-    )
-    result.mounts = _merge_mounts(
-        result.mounts,
-        profile.mounts or [],
-        result.mount_overrides,
-        profile.name,
-    )
-    result.git_mounts = _merge_git_mounts(
-        result.git_mounts,
-        profile.git_mounts or [],
-        profile.name,
-    )
-    return result
-
-
-async def resolve_profile(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-) -> ResolvedProfile:
-    """Resolve a config profile with all includes.
-
-    Args:
-        session: Database session.
-        profile_id: Profile ID to resolve.
-
-    Returns:
-        ResolvedProfile with merged env vars, runtime hints, mounts, and files.
-
-    Raises:
-        ConfigProfileCycleError: If a cycle is detected in includes.
-        ConfigProfileNotFoundError: If the profile is not found.
-    """
-    return await _resolve_profile_recursive(session, profile_id, set(), [])
-
-
-async def check_include_cycle(
-    session: AsyncSession,
-    profile_id: uuid.UUID,
-    new_include_id: uuid.UUID | None = None,
-) -> list[uuid.UUID] | None:
-    """Check if adding an include would create a cycle.
-
-    Used at save time to validate include relationships before persisting.
-
-    Args:
-        session: Database session.
-        profile_id: The profile that would receive the new include.
-        new_include_id: Optional new profile to include. If None, checks existing includes.
-
-    Returns:
-        The cycle path as a list of UUIDs if a cycle exists, otherwise None.
-    """
-
-    async def _check_from(
-        current_id: uuid.UUID,
-        target_id: uuid.UUID,
-        visited: set[uuid.UUID],
-        path: list[uuid.UUID],
-    ) -> list[uuid.UUID] | None:
-        if current_id in visited:
-            if current_id == target_id:
-                return path + [current_id]
-            return None
-        if current_id == target_id and path:
-            return path + [current_id]
-
-        new_visited = visited | {current_id}
-        new_path = path + [current_id]
-
-        include_query = (
-            select(ConfigProfileInclude)
-            .where(ConfigProfileInclude.profile_id == current_id)
-            .order_by(ConfigProfileInclude.order_index)
-        )
-        include_result = await session.execute(include_query)
-        includes = include_result.scalars().all()
-
-        for include in includes:
-            cycle = await _check_from(
-                include.included_profile_id, target_id, new_visited, new_path
-            )
-            if cycle is not None:
-                return cycle
-        return None
-
-    # Check if new_include_id can reach profile_id (would create cycle)
-    if new_include_id is not None:
-        cycle = await _check_from(new_include_id, profile_id, set(), [])
-        if cycle is not None:
-            return cycle
-
-    # Also check existing includes for cycles
-    cycle = await _check_from(profile_id, profile_id, set(), [])
-    if cycle is not None and len(cycle) > 1:
-        return cycle
-
-    return None
-
-
-def apply_resolved_profile(
-    instance_dir: str,
-    resolved: ResolvedProfile,
-    home_dir: str = "/root",
-) -> tuple[dict[str, str], dict[str, str], list[dict], dict[str, Any]]:
-    """Apply a resolved profile to an instance directory.
-
-    Stages files, writes env vars, and prepares mount volumes.
-
-    Args:
-        instance_dir: Path to the instance directory.
-        resolved: The resolved profile.
-
-    Returns:
-        Tuple of (env_vars, files, volume_mounts, runtime_hints).
-        env_vars: Merged environment variables.
-        files: Relative file paths to content for the instance.
-        volume_mounts: List of Docker volume mount dicts.
-        runtime_hints: Extracted runtime hints.
-    """
-    from pathlib import Path
-
-    instance_path = Path(instance_dir)
-    env_vars = dict(resolved.env_vars)
-    files = dict(resolved.files)
-    volume_mounts = []
-
-    # Write profile files to instance directory
-    for file_path, content in files.items():
-        full_path = instance_path / file_path
-        try:
-            full_path.resolve().relative_to(instance_path.resolve())
-        except ValueError:
-            logger.warning(
-                "Profile file path escapes instance directory: %s", file_path
-            )
-            continue
-        full_path.parent.mkdir(parents=True, exist_ok=True)
-        full_path.write_text(content)
-
-    # Stage mount files and prepare volume mounts
-    for mount in resolved.mounts.values():
-        expanded_target = expand_container_path(mount.target, home_dir)
-        mount_dir = (
-            instance_path / "mounts" / expanded_target.lstrip("/").replace("/", "_")
-        )
-        mount_dir.mkdir(parents=True, exist_ok=True)
-
-        for file_path, content in mount.files.items():
-            full_path = mount_dir / file_path
-            try:
-                full_path.resolve().relative_to(mount_dir.resolve())
-            except ValueError:
-                logger.warning("Mount file path escapes mount directory: %s", file_path)
-                continue
-            full_path.parent.mkdir(parents=True, exist_ok=True)
-            full_path.write_text(content)
-
-            # Mount each file individually so sibling files from other mounts
-            # (e.g. git repo directories) are preserved.
-            file_target = os.path.join(expanded_target, file_path)
-            volume_mounts.append(
-                {
-                    "source": str(full_path),
-                    "target": file_target,
-                    "type": "bind",
-                }
-            )
-
-    return env_vars, files, volume_mounts, resolved.runtime_hints
-
-
-def expand_container_path(path: str, home_dir: str) -> str:
-    """Expand ~ and $HOME in a container path to the actual home directory.
-
-    Only expands at the start of the path (e.g., ~/foo, $HOME/foo, $HOME).
-    Leaves mid-string occurrences unchanged.
-
-    Args:
-        path: Container path that may contain ~ or $HOME.
-        home_dir: The container's home directory (e.g., /home/user or /root).
-
-    Returns:
-        Path with ~ and $HOME expanded.
-    """
-    if path.startswith("~/"):
-        return os.path.join(home_dir, path[2:])
-    if path == "~":
-        return home_dir
-    if path.startswith("$HOME/"):
-        return home_dir + "/" + path[6:]
-    if path == "$HOME":
-        return home_dir
-    return path
-
-
-def resolved_profile_to_dict(resolved: ResolvedProfile) -> dict[str, Any]:
-    """Convert a ResolvedProfile to a plain dict for serialization.
-
-    Args:
-        resolved: The resolved profile.
-
-    Returns:
-        Dict with env_vars, runtime_hints, mounts, files, and metadata.
-    """
-    return {
-        "profile_id": str(resolved.profile_id),
-        "profile_name": resolved.profile_name,
-        "env_vars": resolved.env_vars,
-        "runtime_hints": resolved.runtime_hints,
-        "mounts": [
-            {
-                "target": m.target,
-                "mode": m.mode,
-                "files": m.files,
-                "overridden_files": m.overridden_files,
-            }
-            for m in resolved.mounts.values()
-        ],
-        "files": resolved.files,
-        "overrides": {
-            "env_vars": resolved.env_overrides,
-            "runtime_hints": resolved.hint_overrides,
-            "files": resolved.file_overrides,
-            "mounts": resolved.mount_overrides,
-        },
-        "git_mounts": resolved.git_mounts,
-        "included_profiles": resolved.included_profiles,
-    }

apps/api/src/services/correlation.py

@@ -1,32 +0,0 @@
-"""Async correlation ID context variable and helpers."""
-
-import contextvars
-import uuid
-
-from fastapi import Request
-from starlette.middleware.base import BaseHTTPMiddleware
-
-CORRELATION_ID: contextvars.ContextVar[str] = contextvars.ContextVar("correlation_id")
-
-
-def get_correlation_id() -> str:
-    """Return the current correlation ID or generate a new UUID."""
-    try:
-        return CORRELATION_ID.get()
-    except LookupError:
-        return str(uuid.uuid4())
-
-
-class CorrelationIdMiddleware(BaseHTTPMiddleware):
-    """Set correlation ID from X-Request-ID header or generate a new UUID."""
-
-    async def dispatch(self, request: Request, call_next):
-        request_id = request.headers.get("X-Request-ID")
-        correlation_id = request_id or str(uuid.uuid4())
-        token = CORRELATION_ID.set(correlation_id)
-        try:
-            response = await call_next(request)
-            response.headers["X-Request-ID"] = correlation_id
-            return response
-        finally:
-            CORRELATION_ID.reset(token)

apps/api/src/services/docker.py

@@ -1,484 +0,0 @@
-"""Docker service for managing tool instances."""
-
-import logging
-import subprocess
-import time
-from collections import Counter
-from pathlib import Path
-from typing import Any
-
-logger = logging.getLogger(__name__)
-
-
-def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
-    """Sort volume strings so parent paths come before child paths.
-
-    Docker Compose mounts volumes in array order. A later mount at a parent
-    path hides earlier mounts at child paths. By sorting shallow paths first
-    and deep paths last, deeper (more specific) mounts overlay correctly.
-
-    Volume format: source:target or source:target:type
-
-    Args:
-        volumes: List of Docker volume mount strings.
-
-    Returns:
-        Sorted list with parent paths before child paths.
-    """
-
-    def _target_depth(vol: str) -> int:
-        parts = vol.split(":")
-        if len(parts) < 2:
-            return 0
-        target = parts[1].rstrip("/")
-        if not target or target == "/":
-            return 0
-        return target.count("/")
-
-    # Detect duplicate targets and warn
-    targets = []
-    for vol in volumes:
-        parts = vol.split(":")
-        targets.append(parts[1] if len(parts) > 1 else "")
-    dupes = [t for t, c in Counter(targets).items() if c > 1]
-    if dupes:
-        logger.warning("Duplicate mount targets detected: %s", dupes)
-
-    # Stable sort: parent paths first, child paths last
-    return sorted(volumes, key=_target_depth)
-
-
-def render_compose_template(template: str, variables: dict[str, Any]) -> str:
-    """Render a Docker Compose template with variable substitution.
-
-    Args:
-        template: The compose template string
-        variables: Dictionary of variable names to values
-
-    Returns:
-        Rendered compose file content
-    """
-    result = template
-    for key, value in variables.items():
-        placeholder = f"{{{{{key}}}}}"
-        result = result.replace(placeholder, str(value))
-    return result
-
-
-def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
-    """Create and return the instance directory path.
-
-    Args:
-        instance_id: Unique instance identifier
-        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
-
-    Returns:
-        Absolute path to instance directory
-    """
-    if base_path is None:
-        from src.config import Settings
-
-        base_path = Settings().instance_base_path
-    instance_dir = Path(base_path) / instance_id
-    instance_dir.mkdir(parents=True, exist_ok=True)
-    return str(instance_dir.absolute())
-
-
-def write_compose_file(instance_dir: str, content: str) -> str:
-    """Write the rendered compose file to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        content: Rendered compose content
-
-    Returns:
-        Path to the compose file
-    """
-    compose_path = Path(instance_dir) / "docker-compose.yml"
-    compose_path.write_text(content)
-    return str(compose_path)
-
-
-def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
-    """Write environment variables to a .env file.
-
-    Args:
-        instance_dir: Path to instance directory
-        env_vars: Dictionary of env var names to values
-
-    Returns:
-        Path to the env file
-    """
-    env_path = Path(instance_dir) / ".env"
-    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
-    env_path.write_text("\n".join(lines) + "\n")
-    return str(env_path)
-
-
-def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
-    """Write config files to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        files: Dictionary of file paths (relative to instance dir) to content
-    """
-    instance_path = Path(instance_dir)
-    for file_path, content in files.items():
-        # Ensure the path is within the instance directory (security)
-        full_path = instance_path / file_path
-        try:
-            full_path.resolve().relative_to(instance_path.resolve())
-        except ValueError:
-            raise ValueError(f"File path '{file_path}' escapes instance directory")
-
-        full_path.parent.mkdir(parents=True, exist_ok=True)
-        full_path.write_text(content)
-
-
-def execute_compose_command(
-    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
-) -> tuple[int, str, str]:
-    """Execute a docker compose command.
-
-    Args:
-        compose_path: Path to docker-compose.yml
-        action: The compose action (up, down, start, stop, restart)
-        timeout: Command timeout in seconds
-        env_file: Optional path to .env file for environment variables
-
-    Returns:
-        Tuple of (returncode, stdout, stderr)
-    """
-    instance_dir = Path(compose_path).parent
-
-    cmd = ["docker", "compose", "-f", compose_path]
-
-    if env_file:
-        cmd.extend(["--env-file", env_file])
-
-    if action == "up":
-        cmd.extend(["up", "-d", "--force-recreate"])
-    elif action == "down":
-        cmd.extend(["down", "-v"])
-    elif action in ("start", "stop", "restart"):
-        cmd.append(action)
-    else:
-        raise ValueError(f"Unknown compose action: {action}")
-
-    result = subprocess.run(
-        cmd,
-        cwd=str(instance_dir),
-        capture_output=True,
-        text=True,
-        timeout=timeout,
-    )
-
-    return result.returncode, result.stdout, result.stderr
-
-
-def get_container_id(instance_name: str) -> str | None:
-    """Get the container ID for a compose service.
-
-    Uses exact name matching to avoid substring collisions with tunnel
-    containers (e.g. tunnel-code-server-... matching code-server-...).
-    Falls back to case-insensitive matching since Docker DNS is case-
-    insensitive but docker inspect is case-sensitive.
-
-    Args:
-        instance_name: The expected container name.
-
-    Returns:
-        Container ID or None if not found.
-    """
-    expected = instance_name.lower()
-
-    # Fast path: exact match via docker inspect
-    result = subprocess.run(
-        ["docker", "inspect", "-f", "{{.Id}}", expected],
-        capture_output=True,
-        text=True,
-    )
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip()
-
-    # Fallback: list all containers and do case-insensitive exact match
-    ps_result = subprocess.run(
-        ["docker", "ps", "-a", "--format", "{{.Names}}\t{{.ID}}"],
-        capture_output=True,
-        text=True,
-    )
-    if ps_result.returncode == 0:
-        for line in ps_result.stdout.strip().splitlines():
-            parts = line.split("\t")
-            if len(parts) == 2:
-                name, cid = parts
-                if name.lower() == expected:
-                    return cid
-    return None
-
-
-def get_container_name(instance_name: str) -> str | None:
-    """Get the full container name for a compose service.
-
-    Uses exact name matching via docker inspect to avoid substring collisions.
-
-    Args:
-        instance_name: The exact container name (case-insensitive for Docker).
-
-    Returns:
-        Container name or None if not found.
-    """
-    result = subprocess.run(
-        ["docker", "inspect", "-f", "{{.Name}}", instance_name.lower()],
-        capture_output=True,
-        text=True,
-    )
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().lstrip("/")
-    return None
-
-
-def get_backend_network_name() -> str:
-    """Auto-detect the actual Docker network name for the backend network.
-
-    Docker Compose prefixes network names with the project directory name
-    (e.g. 'headquarter_backend' instead of 'backend'). We inspect the API
-    container itself to find the real network name it's connected to.
-
-    Returns:
-        The actual Docker network name, or 'backend' as fallback.
-    """
-    # Try to find the API container by its known name
-    api_container = "hq-api"
-    result = subprocess.run(
-        [
-            "docker",
-            "inspect",
-            "-f",
-            "{{range $k, $v := .NetworkSettings.Networks}}{{$k}} {{end}}",
-            api_container,
-        ],
-        capture_output=True,
-        text=True,
-    )
-    if result.returncode == 0 and result.stdout.strip():
-        networks = result.stdout.strip().split()
-        for net in networks:
-            if "backend" in net.lower():
-                return net
-        # API container is on some network — return the first one
-        return networks[0]
-    return "backend"
-
-
-def connect_container_to_network(
-    container_name: str, network_name: str | None = None
-) -> bool:
-    """Connect a Docker container to an existing network.
-
-    Args:
-        container_name: Name or ID of the container
-        network_name: Name of the Docker network. If None, auto-detects
-            from the API container's own network membership.
-
-    Returns:
-        True if successful, False otherwise
-    """
-    if network_name is None:
-        network_name = get_backend_network_name()
-    result = subprocess.run(
-        ["docker", "network", "connect", network_name, container_name],
-        capture_output=True,
-        text=True,
-    )
-    return result.returncode == 0
-
-
-def get_container_ip_on_network(
-    container_id: str, network_name: str | None = None
-) -> str | None:
-    """Get a container's IP address on a specific Docker network.
-
-    Args:
-        container_id: Docker container ID or name.
-        network_name: Network name. If None, auto-detects from the API container.
-
-    Returns:
-        IP address string, or None if the container is not on that network.
-    """
-    if network_name is None:
-        network_name = get_backend_network_name()
-    result = subprocess.run(
-        [
-            "docker",
-            "inspect",
-            "-f",
-            f"{{{{.NetworkSettings.Networks.{network_name}.IPAddress}}}}",
-            container_id,
-        ],
-        capture_output=True,
-        text=True,
-    )
-    if result.returncode == 0:
-        ip = result.stdout.strip()
-        if ip and ip != "<no value>":
-            return ip
-    return None
-
-
-def is_container_on_network(container_id: str, network_name: str | None = None) -> bool:
-    """Check whether a container is already attached to a Docker network.
-
-    Args:
-        container_id: Docker container ID or name.
-        network_name: Network name. If None, auto-detects from the API container.
-
-    Returns:
-        True if the container is on the network.
-    """
-    if network_name is None:
-        network_name = get_backend_network_name()
-    result = subprocess.run(
-        [
-            "docker",
-            "inspect",
-            "-f",
-            f"{{{{.NetworkSettings.Networks.{network_name}}}}}",
-            container_id,
-        ],
-        capture_output=True,
-        text=True,
-    )
-    return result.returncode == 0 and "<no value>" not in result.stdout
-
-
-def get_container_status(container_id: str) -> dict[str, Any]:
-    """Get the status of a Docker container.
-
-    Args:
-        container_id: Docker container ID
-
-    Returns:
-        Dict with 'status' (running, exited, restarting, not_found),
-        'exit_code' (int or None), and 'health' (health status or None)
-    """
-    result = subprocess.run(
-        [
-            "docker",
-            "inspect",
-            "-f",
-            "{{.State.Status}}|{{.State.ExitCode}}|{{if .State.Health}}{{.State.Health.Status}}{{else}}none{{end}}",
-            container_id,
-        ],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode != 0:
-        return {"status": "not_found", "exit_code": None, "health": None}
-
-    parts = result.stdout.strip().split("|")
-    status = parts[0] if parts else "unknown"
-    exit_code = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else None
-    health = parts[2] if len(parts) > 2 and parts[2] != "none" else None
-
-    return {"status": status, "exit_code": exit_code, "health": health}
-
-
-def wait_for_container_running(
-    container_id: str, timeout: int = 30, interval: float = 2.0
-) -> dict[str, Any]:
-    """Wait for a container to reach the running state.
-
-    Polls docker inspect until the container status is "running" or timeout.
-
-    Args:
-        container_id: Docker container ID
-        timeout: Maximum seconds to wait
-        interval: Seconds between polls
-
-    Returns:
-        Dict with 'success' (bool), 'status' (str), 'exit_code' (int or None),
-        and 'waited_seconds' (float)
-    """
-
-    start_time = time.time()
-
-    while time.time() - start_time < timeout:
-        info = get_container_status(container_id)
-
-        if info["status"] == "running":
-            return {
-                "success": True,
-                "status": "running",
-                "exit_code": None,
-                "waited_seconds": time.time() - start_time,
-            }
-
-        if info["status"] == "exited":
-            return {
-                "success": False,
-                "status": "exited",
-                "exit_code": info["exit_code"],
-                "waited_seconds": time.time() - start_time,
-            }
-
-        if info["status"] == "not_found":
-            return {
-                "success": False,
-                "status": "not_found",
-                "exit_code": None,
-                "waited_seconds": time.time() - start_time,
-            }
-
-        time.sleep(interval)
-
-    # Timeout reached
-    info = get_container_status(container_id)
-    return {
-        "success": False,
-        "status": info["status"],
-        "exit_code": info["exit_code"],
-        "waited_seconds": time.time() - start_time,
-    }
-
-
-def get_container_logs(container_id: str, tail: int = 100) -> str:
-    """Get the logs of a Docker container.
-
-    Args:
-        container_id: Docker container ID
-        tail: Number of lines to return
-
-    Returns:
-        Container logs
-    """
-    result = subprocess.run(
-        ["docker", "logs", "--tail", str(tail), container_id],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0:
-        return result.stdout
-    return f"Failed to get logs: {result.stderr}"
-
-
-def find_free_port(start: int = 10000, end: int = 20000) -> int:
-    """Find a free TCP port in the given range.
-
-    Args:
-        start: Start of port range
-        end: End of port range
-
-    Returns:
-        Free port number
-    """
-    import socket
-
-    for port in range(start, end):
-        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-            if s.connect_ex(("localhost", port)) != 0:
-                return port
-
-    raise RuntimeError(f"No free port found in range {start}-{end}")

apps/api/src/services/event_bus.py

@@ -1,97 +0,0 @@
-"""In-memory typed event bus for instance lifecycle and health events."""
-
-import asyncio
-import inspect
-import logging
-import uuid
-from collections.abc import Awaitable, Callable
-from typing import Any
-
-logger = logging.getLogger(__name__)
-
-InstanceEventPayload = dict[str, Any]
-EventCallback = Callable[[InstanceEventPayload], Awaitable[None] | None]  # noqa: UP044
-
-
-class InstanceEventBus:
-    """Singleton in-memory event bus with typed pub/sub and exception isolation."""
-
-    _instance: "InstanceEventBus | None" = None
-    _lock: asyncio.Lock = asyncio.Lock()
-
-    def __init__(self) -> None:
-        self._subscribers: dict[str, list[tuple[str, EventCallback]]] = {}
-
-    def __new__(cls) -> "InstanceEventBus":
-        if cls._instance is None:
-            cls._instance = super().__new__(cls)
-            cls._instance._subscribers = {}
-        return cls._instance
-
-    def _reset_for_testing(self) -> None:
-        """Clear all subscribers. For test use only."""
-        self._subscribers.clear()
-
-    def subscribe(
-        self,
-        event_type: str,
-        callback: EventCallback,
-    ) -> Callable[[], None]:
-        """Register a callback for an event type.
-
-        Args:
-            event_type: The event type to subscribe to.
-            callback: A sync or async callable that receives the payload.
-
-        Returns:
-            An unsubscribe function.
-        """
-        if event_type not in self._subscribers:
-            self._subscribers[event_type] = []
-        callback_id = str(uuid.uuid4())
-        self._subscribers[event_type].append((callback_id, callback))
-
-        def unsubscribe() -> None:
-            self.unsubscribe(event_type, callback_id)
-
-        return unsubscribe
-
-    def unsubscribe(self, event_type: str, callback_id: str) -> None:
-        """Remove a specific callback by ID."""
-        if event_type in self._subscribers:
-            self._subscribers[event_type] = [
-                (cid, cb)
-                for cid, cb in self._subscribers[event_type]
-                if cid != callback_id
-            ]
-            if not self._subscribers[event_type]:
-                del self._subscribers[event_type]
-
-    def unsubscribe_all(self, event_type: str) -> None:
-        """Remove all subscribers for an event type."""
-        self._subscribers.pop(event_type, None)
-
-    async def publish(self, event_type: str, payload: InstanceEventPayload) -> None:
-        """Deliver payload to all subscribers of event_type.
-
-        Also delivers to subscribers registered under the wildcard "*".
-        Exceptions from individual subscribers are caught and logged;
-        delivery continues to remaining subscribers.
-        """
-        callbacks: list[tuple[str, EventCallback]] = []
-        callbacks.extend(self._subscribers.get(event_type, []))
-        callbacks.extend(self._subscribers.get("*", []))
-
-        for _callback_id, callback in callbacks:
-            try:
-                if inspect.iscoroutinefunction(callback):
-                    await callback(payload)
-                else:
-                    callback(payload)
-            except Exception:
-                correlation_id = payload.get("correlation_id", "unknown")
-                logger.exception(
-                    "Event subscriber failed for %s",
-                    event_type,
-                    extra={"correlation_id": correlation_id},
-                )

apps/api/src/services/file_service.py

@@ -1,128 +0,0 @@
-"""File operations scoped to a workspace directory."""
-
-import logging
-import os
-from dataclasses import dataclass
-
-from src.models.workspace import Workspace
-
-logger = logging.getLogger(__name__)
-
-
-@dataclass
-class FileEntry:
-    """A single file or directory entry."""
-
-    name: str
-    path: str
-    type: str  # "file" or "directory"
-    size: int | None = None
-
-
-class FileService:
-    """Read and write files within a workspace directory."""
-
-    def list_directory(
-        self,
-        workspace: Workspace,
-        relative_path: str = "",
-    ) -> list[FileEntry]:
-        """List entries in a workspace directory.
-
-        Args:
-            workspace: The workspace to list files in.
-            relative_path: Path relative to workspace root.
-
-        Returns:
-            List of file entries sorted by name (directories first).
-        """
-        abs_path = os.path.join(workspace.path, relative_path)
-        abs_path = os.path.normpath(abs_path)
-
-        # Security: ensure we stay within workspace
-        if not abs_path.startswith(os.path.normpath(workspace.path)):
-            raise ValueError("Path escapes workspace directory")
-
-        if not os.path.exists(abs_path):
-            return []
-
-        entries = []
-        for item in sorted(os.listdir(abs_path)):
-            full = os.path.join(abs_path, item)
-            rel = os.path.join(relative_path, item) if relative_path else item
-            is_dir = os.path.isdir(full)
-            size = os.path.getsize(full) if os.path.isfile(full) else None
-            entries.append(
-                FileEntry(
-                    name=item,
-                    path=rel.replace("\\", "/"),
-                    type="directory" if is_dir else "file",
-                    size=size,
-                )
-            )
-
-        # Directories first, then files, both alphabetical
-        entries.sort(key=lambda e: (0 if e.type == "directory" else 1, e.name.lower()))
-        return entries
-
-    def read_file(self, workspace: Workspace, relative_path: str) -> str:
-        """Read a text file from the workspace.
-
-        Args:
-            workspace: The workspace to read from.
-            relative_path: Path relative to workspace root.
-
-        Returns:
-            File contents as string.
-
-        Raises:
-            ValueError: If path escapes workspace or file is binary.
-            FileNotFoundError: If file does not exist.
-        """
-        abs_path = self._resolve_path(workspace, relative_path)
-
-        if not os.path.isfile(abs_path):
-            raise FileNotFoundError(f"Not a file: {relative_path}")
-
-        # Basic binary check — read first 8KB and look for null bytes
-        with open(abs_path, "rb") as f:
-            chunk = f.read(8192)
-            if b"\x00" in chunk:
-                raise ValueError("Binary files cannot be viewed")
-
-        with open(abs_path, encoding="utf-8", errors="replace") as f:
-            return f.read()
-
-    def write_file(
-        self,
-        workspace: Workspace,
-        relative_path: str,
-        content: str,
-    ) -> None:
-        """Write a text file to the workspace.
-
-        Args:
-            workspace: The workspace to write to.
-            relative_path: Path relative to workspace root.
-            content: File contents.
-
-        Raises:
-            ValueError: If path escapes workspace.
-        """
-        abs_path = self._resolve_path(workspace, relative_path)
-        os.makedirs(os.path.dirname(abs_path), exist_ok=True)
-
-        with open(abs_path, "w", encoding="utf-8") as f:
-            f.write(content)
-
-        logger.info("Wrote file %s in workspace %s", relative_path, workspace.id)
-
-    def _resolve_path(self, workspace: Workspace, relative_path: str) -> str:
-        """Resolve a relative path to absolute, with security check."""
-        abs_path = os.path.normpath(os.path.join(workspace.path, relative_path))
-        workspace_root = os.path.normpath(workspace.path)
-
-        if not abs_path.startswith(workspace_root):
-            raise ValueError("Path escapes workspace directory")
-
-        return abs_path

apps/api/src/services/git_operations.py

@@ -1,223 +0,0 @@
-"""Git commands scoped to a workspace directory."""
-
-import asyncio
-import logging
-from dataclasses import dataclass
-
-from src.models.workspace import Workspace
-
-logger = logging.getLogger(__name__)
-
-
-@dataclass
-class GitStatus:
-    """Parsed git status output."""
-
-    branch: str
-    modified: list[str]
-    added: list[str]
-    deleted: list[str]
-    untracked: list[str]
-    ahead: int = 0
-    behind: int = 0
-
-
-@dataclass
-class Commit:
-    """A single git commit."""
-
-    hash: str
-    message: str
-    author: str
-    date: str
-
-
-class GitOperations:
-    """Run git commands within a workspace directory."""
-
-    def __init__(self, workspace: Workspace) -> None:
-        self.cwd = workspace.path
-        self.branch = workspace.branch
-
-    async def _run(self, *cmd: str) -> tuple[int, str, str]:
-        """Run a git command and return (returncode, stdout, stderr)."""
-        proc = await asyncio.create_subprocess_exec(
-            *cmd,
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-        stdout, stderr = await proc.communicate()
-        return proc.returncode or 0, stdout.decode(), stderr.decode()
-
-    async def status(self) -> GitStatus:
-        """Get git status for the workspace."""
-        returncode, stdout, _ = await self._run(
-            "git", "-C", self.cwd, "status", "--porcelain", "-b"
-        )
-
-        modified: list[str] = []
-        added: list[str] = []
-        deleted: list[str] = []
-        untracked: list[str] = []
-        branch = self.branch
-        ahead = 0
-        behind = 0
-
-        for line in stdout.splitlines():
-            if line.startswith("##"):
-                # Branch info line
-                branch_info = line[3:].strip()
-                if "..." in branch_info:
-                    branch = branch_info.split("...")[0]
-                    if "[ahead " in branch_info:
-                        ahead_str = branch_info.split("[ahead ")[1].split("]")[0]
-                        ahead = int(ahead_str.split(",")[0])
-                    if "[behind " in branch_info:
-                        behind_str = branch_info.split("[behind ")[1].split("]")[0]
-                        behind = int(behind_str.split(",")[0])
-                else:
-                    branch = branch_info
-                continue
-
-            if len(line) < 3:
-                continue
-
-            status_code = line[:2]
-            file_path = line[3:]
-
-            # XY format: X = index status, Y = working tree status
-            if status_code == "??":
-                untracked.append(file_path)
-            elif status_code[1] == "D" or status_code[0] == "D":
-                deleted.append(file_path)
-            elif status_code[0] == "A" or status_code[1] == "A":
-                added.append(file_path)
-            else:
-                modified.append(file_path)
-
-        return GitStatus(
-            branch=branch,
-            modified=modified,
-            added=added,
-            deleted=deleted,
-            untracked=untracked,
-            ahead=ahead,
-            behind=behind,
-        )
-
-    async def commit(self, message: str) -> None:
-        """Stage all changes and commit."""
-        rc, _, err = await self._run("git", "-C", self.cwd, "add", "-A")
-        if rc != 0:
-            raise RuntimeError(f"Git add failed: {err}")
-
-        rc, _, err = await self._run("git", "-C", self.cwd, "commit", "-m", message)
-        if rc != 0:
-            raise RuntimeError(f"Git commit failed: {err}")
-
-        logger.info("Committed in workspace: %s", self.cwd)
-
-    async def push(self) -> None:
-        """Push current branch to origin."""
-        rc, _, err = await self._run(
-            "git", "-C", self.cwd, "push", "origin", self.branch
-        )
-        if rc != 0:
-            raise RuntimeError(f"Git push failed: {err}")
-
-        logger.info("Pushed branch %s from workspace: %s", self.branch, self.cwd)
-
-    async def pull(self) -> None:
-        """Pull current branch from origin."""
-        rc, _, err = await self._run(
-            "git", "-C", self.cwd, "pull", "origin", self.branch
-        )
-        if rc != 0:
-            raise RuntimeError(f"Git pull failed: {err}")
-
-        logger.info("Pulled branch %s in workspace: %s", self.branch, self.cwd)
-
-    async def fetch(self) -> None:
-        """Fetch from origin."""
-        rc, _, err = await self._run("git", "-C", self.cwd, "fetch", "origin")
-        if rc != 0:
-            raise RuntimeError(f"Git fetch failed: {err}")
-
-        logger.info("Fetched origin for workspace: %s", self.cwd)
-
-    async def checkout(self, branch: str) -> None:
-        """Checkout a branch."""
-        rc, _, err = await self._run("git", "-C", self.cwd, "checkout", branch)
-        if rc != 0:
-            raise RuntimeError(f"Git checkout failed: {err}")
-
-        self.branch = branch
-        logger.info("Checked out branch %s in workspace: %s", branch, self.cwd)
-
-    async def history(self, path: str | None = None, limit: int = 50) -> list[Commit]:
-        """Get commit history.
-
-        Args:
-            path: Optional file path to filter history.
-            limit: Maximum number of commits.
-
-        Returns:
-            List of commits.
-        """
-        cmd = [
-            "git",
-            "-C",
-            self.cwd,
-            "log",
-            f"--max-count={limit}",
-            "--pretty=format:%H|%s|%an|%ad",
-            "--date=iso",
-        ]
-        if path:
-            cmd.extend(["--", path])
-
-        rc, stdout, err = await self._run(*cmd)
-        if rc != 0:
-            raise RuntimeError(f"Git log failed: {err}")
-
-        commits = []
-        for line in stdout.strip().splitlines():
-            parts = line.split("|", 3)
-            if len(parts) >= 4:
-                commits.append(
-                    Commit(
-                        hash=parts[0],
-                        message=parts[1],
-                        author=parts[2],
-                        date=parts[3],
-                    )
-                )
-
-        return commits
-
-    async def branches(self) -> tuple[list[str], str]:
-        """List all branches and current branch.
-
-        Returns:
-            Tuple of (all_branches, current_branch).
-        """
-        rc, stdout, err = await self._run(
-            "git", "-C", self.cwd, "branch", "-a", "--format=%(refname:short)"
-        )
-        if rc != 0:
-            raise RuntimeError(f"Git branch failed: {err}")
-
-        branches = []
-        current = self.branch
-        for line in stdout.strip().splitlines():
-            line = line.strip()
-            if line.startswith("HEAD") or line.endswith("/HEAD"):
-                continue
-            if line.startswith("remotes/origin/"):
-                branch_name = line.replace("remotes/origin/", "")
-                if branch_name not in branches:
-                    branches.append(branch_name)
-            elif line and line not in branches:
-                branches.append(line)
-
-        return branches, current

apps/api/src/services/git_service.py

@@ -1,176 +0,0 @@
-"""Git operations for workspace management."""
-
-import asyncio
-import logging
-import os
-import subprocess
-import tempfile
-
-logger = logging.getLogger(__name__)
-
-
-class GitService:
-    """Low-level git operations for creating and syncing workspaces."""
-
-    @staticmethod
-    def _prepare_ssh_env(
-        ssh_key: str | None,
-    ) -> tuple[dict[str, str] | None, str | None]:
-        """Prepare environment for git commands with SSH authentication.
-
-        Returns a tuple of (env_dict, temp_key_path). Caller must clean up key_path.
-        """
-        if not ssh_key:
-            return None, None
-
-        fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
-        try:
-            os.write(fd, ssh_key.encode())
-        finally:
-            os.close(fd)
-        os.chmod(key_path, 0o600)
-
-        env = {
-            "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
-        }
-        return env, key_path
-
-    @staticmethod
-    async def clone(
-        remote_url: str, branch: str, path: str, ssh_key: str | None = None
-    ) -> None:
-        """Clone a repository to the given path.
-
-        Args:
-            remote_url: The git remote URL.
-            branch: The branch to clone.
-            path: The destination path for the clone.
-            ssh_key: Optional decrypted SSH private key for authentication.
-
-        Raises:
-            RuntimeError: If the clone fails.
-        """
-        cmd = [
-            "git",
-            "clone",
-            "--branch",
-            branch,
-            "--single-branch",
-            remote_url,
-            path,
-        ]
-
-        env, key_path = GitService._prepare_ssh_env(ssh_key)
-        try:
-            proc = await asyncio.create_subprocess_exec(
-                *cmd,
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-                env={**os.environ, **env} if env else None,
-            )
-            stdout, stderr = await proc.communicate()
-            if proc.returncode != 0:
-                error_msg = stderr.decode().strip() if stderr else "unknown error"
-                logger.error("Git clone failed: %s", error_msg)
-                raise RuntimeError(f"Git clone failed: {error_msg}")
-            logger.debug("Cloned %s (branch: %s) to %s", remote_url, branch, path)
-        finally:
-            if key_path and os.path.exists(key_path):
-                os.unlink(key_path)
-
-    @staticmethod
-    async def fetch(path: str, ssh_key: str | None = None) -> None:
-        """Fetch from origin.
-
-        Args:
-            path: The path to the local git repository.
-            ssh_key: Optional decrypted SSH private key for authentication.
-
-        Raises:
-            RuntimeError: If fetch fails.
-        """
-        env, key_path = GitService._prepare_ssh_env(ssh_key)
-        try:
-            proc = await asyncio.create_subprocess_exec(
-                "git",
-                "-C",
-                path,
-                "fetch",
-                "origin",
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-                env={**os.environ, **env} if env else None,
-            )
-            stdout, stderr = await proc.communicate()
-            if proc.returncode != 0:
-                error_msg = stderr.decode().strip() if stderr else "unknown error"
-                logger.error("Git fetch failed: %s", error_msg)
-                raise RuntimeError(f"Git fetch failed: {error_msg}")
-            logger.debug("Fetched origin for %s", path)
-        finally:
-            if key_path and os.path.exists(key_path):
-                os.unlink(key_path)
-
-    @staticmethod
-    async def pull(path: str, branch: str, ssh_key: str | None = None) -> None:
-        """Pull latest changes from origin.
-
-        Args:
-            path: The path to the local git repository.
-            branch: The branch to pull.
-            ssh_key: Optional decrypted SSH private key for authentication.
-
-        Raises:
-            RuntimeError: If pull fails.
-        """
-        env, key_path = GitService._prepare_ssh_env(ssh_key)
-        try:
-            proc = await asyncio.create_subprocess_exec(
-                "git",
-                "-C",
-                path,
-                "pull",
-                "origin",
-                branch,
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-                env={**os.environ, **env} if env else None,
-            )
-            stdout, stderr = await proc.communicate()
-            if proc.returncode != 0:
-                error_msg = stderr.decode().strip() if stderr else "unknown error"
-                logger.error("Git pull failed: %s", error_msg)
-                raise RuntimeError(f"Git pull failed: {error_msg}")
-            logger.debug("Pulled origin/%s for %s", branch, path)
-        finally:
-            if key_path and os.path.exists(key_path):
-                os.unlink(key_path)
-
-    @staticmethod
-    def branch_exists_remotely(
-        path: str, branch: str, ssh_key: str | None = None
-    ) -> bool:
-        """Check if a branch exists on the remote.
-
-        Args:
-            path: The path to the local git repository.
-            branch: The branch name to check.
-            ssh_key: Optional decrypted SSH private key for authentication.
-
-        Returns:
-            True if the branch exists on origin, False otherwise.
-        """
-        env, key_path = GitService._prepare_ssh_env(ssh_key)
-        try:
-            result = subprocess.run(
-                ["git", "-C", path, "ls-remote", "--heads", "origin", branch],
-                capture_output=True,
-                text=True,
-                env={**os.environ, **env} if env else None,
-            )
-            exists = result.returncode == 0 and result.stdout.strip() != ""
-            logger.debug("Branch %s exists on remote: %s", branch, exists)
-            return exists
-        finally:
-            if key_path and os.path.exists(key_path):
-                os.unlink(key_path)

apps/api/src/services/health_monitor.py

@@ -1,254 +0,0 @@
-"""Background health monitor that polls container and tunnel health."""
-
-import asyncio
-import logging
-import uuid
-from dataclasses import dataclass
-from datetime import datetime, timezone
-
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.database import SessionLocal
-from src.models.health_check import HealthCheck
-from src.models.tool_instance import ToolInstance
-from src.services.correlation import get_correlation_id
-from src.services.docker import get_container_status
-from src.services.tunnel import check_tunnel_health
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.notification_service import notification_service
-
-logger = logging.getLogger(__name__)
-
-
-@dataclass
-class HealthSnapshot:
-    """In-memory snapshot of an instance's health state."""
-
-    container_status: str | None = None
-    container_healthy: bool | None = None
-    tunnel_healthy: bool | None = None
-    exit_code: int | None = None
-
-
-class HealthMonitor:
-    """Polls container and tunnel health, publishing events on state changes."""
-
-    POLL_INTERVAL_SECONDS: float = 15.0
-    _MONITORED_STATUSES: set[str] = {"starting", "running", "unhealthy"}
-
-    def __init__(self, event_bus: InstanceEventBus) -> None:
-        self._event_bus = event_bus
-        self._task: asyncio.Task | None = None
-        self._last_known_state: dict[uuid.UUID, HealthSnapshot] = {}
-
-    def start(self) -> None:
-        """Idempotent start of the background polling task."""
-        if self._task is not None and not self._task.done():
-            return
-        try:
-            loop = asyncio.get_running_loop()
-            self._task = loop.create_task(self._poll_loop())
-        except RuntimeError:
-            pass
-
-    def stop(self) -> None:
-        """Cancel the background task and clear state."""
-        if self._task is not None and not self._task.done():
-            self._task.cancel()
-        self._last_known_state.clear()
-        self._task = None
-
-    async def _poll_loop(self) -> None:
-        """Main polling loop."""
-        while True:
-            try:
-                await asyncio.sleep(self.POLL_INTERVAL_SECONDS)
-                await self._run_check_cycle()
-            except asyncio.CancelledError:
-                break
-            except Exception:
-                logger.exception("Health monitor poll loop error")
-
-    async def _run_check_cycle(self) -> None:
-        """Check all monitored instances in one cycle."""
-        async with SessionLocal() as session:
-            result = await session.execute(
-                select(ToolInstance).where(
-                    ToolInstance.status.in_(self._MONITORED_STATUSES)
-                )
-            )
-            instances = result.scalars().all()
-
-        for instance in instances:
-            async with SessionLocal() as session:
-                await self._check_instance(session, instance)
-
-    async def _check_instance(
-        self,
-        session: AsyncSession,
-        instance: ToolInstance,
-    ) -> None:
-        """Check a single instance and handle state transitions."""
-        try:
-            container_info = get_container_status(instance.container_id or "")
-        except Exception:
-            logger.exception(
-                "Health check failed for instance %s",
-                instance.id,
-                extra={
-                    "instance_id": str(instance.id),
-                    "correlation_id": get_correlation_id(),
-                },
-            )
-            return
-
-        container_status = container_info["status"]
-        exit_code = container_info["exit_code"]
-        container_healthy = (
-            container_info["health"] == "healthy" if container_info["health"] else None
-        )
-
-        tunnel_healthy: bool | None = None
-        if instance.public_url and container_status == "running":
-            try:
-                tunnel_result = check_tunnel_health(instance.public_url)
-                tunnel_healthy = tunnel_result.get("healthy", False)
-            except Exception:
-                logger.exception(
-                    "Tunnel health check failed for instance %s",
-                    instance.id,
-                    extra={
-                        "instance_id": str(instance.id),
-                        "correlation_id": get_correlation_id(),
-                    },
-                )
-                tunnel_healthy = False
-
-        snapshot = HealthSnapshot(
-            container_status=container_status,
-            container_healthy=container_healthy,
-            tunnel_healthy=tunnel_healthy,
-            exit_code=exit_code,
-        )
-
-        previous = self._last_known_state.get(instance.id)
-
-        # Determine new status
-        new_status = self._derive_status(snapshot)
-
-        # If first check or state changed
-        if previous is None or not self._snapshots_equal(previous, snapshot):
-            await self._handle_state_change(
-                session, instance, previous, snapshot, new_status
-            )
-            self._last_known_state[instance.id] = snapshot
-
-    def _derive_status(self, snapshot: HealthSnapshot) -> str:
-        """Derive instance status from health snapshot."""
-        if snapshot.container_status != "running":
-            return "error"
-        if snapshot.tunnel_healthy is False:
-            return "unhealthy"
-        return "running"
-
-    def _snapshots_equal(self, a: HealthSnapshot, b: HealthSnapshot) -> bool:
-        """Compare two snapshots for equality."""
-        return (
-            a.container_status == b.container_status
-            and a.container_healthy == b.container_healthy
-            and a.tunnel_healthy == b.tunnel_healthy
-            and a.exit_code == b.exit_code
-        )
-
-    async def _handle_state_change(
-        self,
-        session: AsyncSession,
-        instance: ToolInstance,
-        previous: HealthSnapshot | None,
-        snapshot: HealthSnapshot,
-        new_status: str,
-    ) -> None:
-        """Update DB, insert health check, and publish event."""
-        previous_status = instance.status
-
-        # Update instance status
-        instance.status = new_status
-        if new_status == "error":
-            instance.last_stopped_at = datetime.now(timezone.utc)
-
-        # Insert health check row
-        health_check = HealthCheck(
-            instance_id=instance.id,
-            container_status=snapshot.container_status,
-            container_healthy=snapshot.container_healthy,
-            tunnel_healthy=snapshot.tunnel_healthy,
-            exit_code=snapshot.exit_code,
-            probe_status=None,
-            probe_output=None,
-        )
-        session.add(health_check)
-        await session.commit()
-
-        # Build event payload
-        correlation_id = get_correlation_id()
-        metadata: dict = {"previous_status": previous_status}
-        if snapshot.exit_code is not None:
-            metadata["exit_code"] = snapshot.exit_code
-            metadata["error_type"] = "container"
-        if instance.public_url:
-            metadata["tunnel_url"] = instance.public_url
-
-        if new_status == "error":
-            event_type = "instance.error"
-            message = f"Container failed with status {snapshot.container_status}"
-            if snapshot.exit_code is not None:
-                message += f" (exit code: {snapshot.exit_code})"
-        else:
-            event_type = "instance.health_changed"
-            message = f"Container is now {new_status}"
-
-        payload: InstanceEventPayload = {
-            "event": event_type,
-            "instance_id": str(instance.id),
-            "status": new_status,
-            "message": message,
-            "metadata": metadata,
-            "timestamp": datetime.now(timezone.utc).isoformat(),
-            "correlation_id": correlation_id,
-        }
-
-        await self._event_bus.publish(event_type, payload)
-
-        # Create notification for instance owner (fire-and-forget)
-        # Only send warnings and errors; skip "recovered" info notifications.
-        if new_status == "error":
-            category = "instance"
-            severity = "error"
-            title = "Container failed"
-        elif new_status == "unhealthy":
-            category = "health"
-            severity = "warning"
-            title = "Container unhealthy"
-        else:
-            # Running/recovered — do not notify
-            return
-
-        try:
-            await notification_service.create_notification(
-                session=session,
-                user_id=instance.owner_id,
-                category=category,
-                severity=severity,
-                title=title,
-                message=message,
-                source_type="tool_instances",
-                source_id=instance.id,
-                metadata=metadata,
-            )
-        except Exception:
-            logger.exception(
-                "Failed to create notification for health event %s",
-                event_type,
-                extra={"correlation_id": correlation_id},
-            )

apps/api/src/services/lifecycle_hooks.py

@@ -1,162 +0,0 @@
-"""Lifecycle hook helpers for instrumenting tool instance transitions."""
-
-import logging
-import uuid
-from datetime import datetime, timezone
-
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.instance_event import InstanceEvent
-from src.models.tool_instance import ToolInstance
-from src.services.correlation import get_correlation_id
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.notification_service import notification_service
-
-logger = logging.getLogger(__name__)
-
-
-def _derive_title(event_type: str) -> str:
-    """Map lifecycle event type to a human-readable notification title."""
-    mapping = {
-        "instance.created": "Container created",
-        "instance.started": "Container started",
-        "instance.stopped": "Container stopped",
-        "instance.restarted": "Container restarted",
-        "instance.deleted": "Container deleted",
-        "instance.error": "Container error",
-        "instance.health_changed": "Container ready",
-    }
-    return mapping.get(
-        event_type,
-        event_type.replace("instance.", "").replace("_", " ").title(),
-    )
-
-
-def _should_notify(event_type: str, status: str | None) -> bool:
-    """Determine whether a lifecycle event should generate a notification.
-
-    Only warnings, errors, and "container is ready" (health_changed running)
-    are sent to users.
-    """
-    if event_type == "instance.error":
-        return True
-    if event_type == "instance.health_changed" and status == "running":
-        return True
-    # Filter out: created, started, stopped, restarted, deleted, and any
-    # health_changed that is not "running" (unhealthy is handled by health_monitor)
-    return False
-
-
-def _build_payload(
-    event_type: str,
-    instance: ToolInstance,
-    status: str | None = None,
-    message: str | None = None,
-    metadata: dict | None = None,
-) -> InstanceEventPayload:
-    """Construct a standard event payload."""
-    return {
-        "event": event_type,
-        "instance_id": str(instance.id),
-        "status": status or instance.status,
-        "message": message,
-        "metadata": metadata or {},
-        "timestamp": datetime.now(timezone.utc).isoformat(),
-        "correlation_id": get_correlation_id(),
-    }
-
-
-async def _write_audit_row(
-    session: AsyncSession,
-    instance: ToolInstance,
-    event_type: str,
-    created_by: uuid.UUID | None = None,
-    status: str | None = None,
-    message: str | None = None,
-    metadata: dict | None = None,
-) -> InstanceEvent:
-    """Persist an instance_events audit row."""
-    row = InstanceEvent(
-        instance_id=instance.id,
-        event_type=event_type.replace("instance.", ""),
-        status=status or instance.status,
-        message=message,
-        created_by=created_by,
-        event_metadata=metadata or {},
-    )
-    session.add(row)
-    await session.commit()
-    return row
-
-
-async def publish_lifecycle_event(
-    event_bus: InstanceEventBus,
-    session: AsyncSession,
-    instance: ToolInstance,
-    event_type: str,
-    created_by: uuid.UUID | None = None,
-    status: str | None = None,
-    message: str | None = None,
-    metadata: dict | None = None,
-) -> None:
-    """Publish a lifecycle event and write an audit row after DB commit.
-
-    Args:
-        event_bus: The global event bus.
-        session: Active async DB session.
-        instance: The affected tool instance.
-        event_type: One of instance.created, instance.started, etc.
-        created_by: User ID for user-initiated actions; None for system.
-        status: Optional status override.
-        message: Optional human-readable message.
-        metadata: Optional extra metadata.
-    """
-    payload = _build_payload(
-        event_type=event_type,
-        instance=instance,
-        status=status,
-        message=message,
-        metadata=metadata,
-    )
-
-    # Write audit row
-    await _write_audit_row(
-        session=session,
-        instance=instance,
-        event_type=event_type,
-        created_by=created_by,
-        status=status or instance.status,
-        message=message,
-        metadata=metadata,
-    )
-
-    # Publish to bus
-    await event_bus.publish(event_type, payload)
-
-    # Create notification for instance owner (fire-and-forget)
-    # Only send warnings, errors, and "container is ready" notifications.
-    effective_status = status or instance.status
-    if not _should_notify(event_type, effective_status):
-        return
-
-    severity = "error" if event_type == "instance.error" else "success"
-    title = _derive_title(event_type)
-
-    try:
-        await notification_service.create_notification(
-            session=session,
-            user_id=instance.owner_id,
-            category="instance",
-            severity=severity,
-            title=title,
-            message=message,
-            source_type="tool_instances",
-            source_id=instance.id,
-            metadata=metadata,
-        )
-    except Exception:
-        logger.exception(
-            "Failed to create notification for lifecycle event %s",
-            event_type,
-            extra={"correlation_id": payload.get("correlation_id", "unknown")},
-        )

apps/api/src/services/manifest_compiler.py

@@ -1,446 +0,0 @@
-"""Manifest compiler: transforms ToolDefinitionManifest into Dockerfile + Compose."""
-
-import hashlib
-import json
-import shlex
-from copy import deepcopy
-from typing import Any
-
-import yaml
-
-from src.services.docker import sort_volumes_by_specificity
-
-
-def resolve_base(manifest: dict) -> dict:
-    """Merge a base definition into a tool manifest.
-
-    If the manifest has base_definition_id, the base manifest is loaded
-    and merged. Tool-specific values override base values.
-
-    Args:
-        manifest: The tool manifest JSON (may reference a base)
-
-    Returns:
-        A fully resolved manifest with base values merged in.
-    """
-    result = deepcopy(manifest)
-
-    base_definition_id = result.pop("base_definition_id", None)
-    result.pop("base_version", None)
-
-    if base_definition_id:
-        # This will be provided by the caller (they have the DB session)
-        # For now, we assume the manifest has been pre-resolved
-        # or the caller provides the base manifest separately.
-        pass
-
-    return result
-
-
-def deep_merge(base: dict, override: dict) -> dict:
-    """Deep merge two manifests. Arrays are concatenated; dicts are merged.
-
-    Args:
-        base: The base manifest.
-        override: The tool-specific overrides.
-
-    Returns:
-        Merged manifest.
-    """
-    merged = deepcopy(base)
-
-    for key, value in override.items():
-        if key == "mounts" and isinstance(value, list):
-            # Concatenate mount arrays
-            existing = merged.get("mounts", [])
-            merged["mounts"] = existing + deepcopy(value)
-        elif key == "scripts" and isinstance(value, dict):
-            # Merge script categories
-            if "scripts" not in merged:
-                merged["scripts"] = {}
-            for script_key, script_value in value.items():
-                existing = merged["scripts"].get(script_key, [])
-                merged["scripts"][script_key] = existing + deepcopy(script_value)
-        elif key == "packages" and isinstance(value, dict):
-            # Union package arrays
-            if "packages" not in merged:
-                merged["packages"] = {}
-            for pkg_key, pkg_value in value.items():
-                if (
-                    pkg_key in merged["packages"]
-                    and isinstance(merged["packages"][pkg_key], list)
-                    and isinstance(pkg_value, list)
-                ):
-                    merged["packages"][pkg_key] = merged["packages"][
-                        pkg_key
-                    ] + deepcopy(pkg_value)
-                else:
-                    merged["packages"][pkg_key] = deepcopy(pkg_value)
-        elif key == "env" and isinstance(value, dict):
-            # Dict merge: override wins on key conflict
-            if "env" not in merged:
-                merged["env"] = {}
-            merged["env"].update(deepcopy(value))
-        elif (
-            isinstance(value, dict) and key in merged and isinstance(merged[key], dict)
-        ):
-            # Generic dict merge
-            merged[key] = {**merged[key], **deepcopy(value)}
-        else:
-            # Override entirely
-            merged[key] = deepcopy(value)
-
-    return merged
-
-
-def compile_dockerfile(manifest: dict) -> str:
-    """Compile a resolved manifest into a Dockerfile string.
-
-    Args:
-        manifest: Fully resolved manifest JSON.
-
-    Returns:
-        Dockerfile content.
-    """
-    lines: list[str] = []
-
-    # FROM
-    base_image = manifest.get("base_image", "ubuntu:24.04")
-    lines.append(f"FROM {base_image}")
-    lines.append("")
-
-    # Build-time environment
-    env = manifest.get("env", {})
-    for key, value in env.items():
-        lines.append(f"ENV {key}={shlex.quote(value)}")
-    if env:
-        lines.append("")
-
-    # System packages (apt)
-    apt_packages = manifest.get("packages", {}).get("apt", [])
-    if manifest.get("user"):
-        # Ensure sudo is available for permission-fixing startup scripts
-        apt_packages = list(apt_packages)
-        if "sudo" not in apt_packages:
-            apt_packages.append("sudo")
-    if apt_packages:
-        lines.append("RUN apt-get update && apt-get install -y \\")
-        for pkg in apt_packages[:-1]:
-            lines.append(f"    {pkg} \\")
-        lines.append(f"    {apt_packages[-1]} \\")
-        lines.append("    && rm -rf /var/lib/apt/lists/*")
-        lines.append("")
-
-    # Node.js
-    node = manifest.get("packages", {}).get("node")
-    if node:
-        version = node.get("version", "20")
-        lines.append(
-            f"RUN curl -fsSL https://deb.nodesource.com/setup_{version}.x | bash - && \\"
-        )
-        lines.append("    apt-get install -y nodejs && \\")
-        lines.append("    rm -rf /var/lib/apt/lists/*")
-        lines.append("")
-
-    # NPM global packages
-    npm_packages = manifest.get("packages", {}).get("npm_global", [])
-    if npm_packages:
-        pkg_list = " ".join(shlex.quote(p) for p in npm_packages)
-        lines.append(f"RUN npm install -g {pkg_list}")
-        lines.append("")
-
-    # Pip packages
-    pip_packages = manifest.get("packages", {}).get("pip", [])
-    if pip_packages:
-        pkg_list = " ".join(shlex.quote(p) for p in pip_packages)
-        lines.append(f"RUN pip install {pkg_list}")
-        lines.append("")
-
-    # User creation
-    user = manifest.get("user")
-    if user:
-        name = user["name"]
-        uid = user["uid"]
-        gid = user["gid"]
-        create_home = "-m " if user.get("create_home", True) else ""
-        shell = user.get("shell", "/bin/bash")
-        lines.append(f"RUN groupadd -g {gid} {name} && \\")
-        lines.append(f"    useradd -u {uid} -g {gid} {create_home}-s {shell} {name}")
-        lines.append("")
-        # Set HOME and USER for runtime compatibility
-        home = f"/home/{name}"
-        lines.append(f"ENV HOME={home}")
-        lines.append(f"ENV USER={name}")
-        lines.append("")
-        # Ensure home directory exists and is writable by the user
-        lines.append(
-            f"RUN mkdir -p {home} && chown {name}:{name} {home} && chmod 755 {home}"
-        )
-        lines.append("")
-
-        # Configure passwordless sudo so startup scripts can fix permissions
-        lines.append(
-            f'RUN echo "{name} ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/{name} && chmod 0440 /etc/sudoers.d/{name}'
-        )
-        lines.append("")
-
-    # Build scripts
-    build_scripts = manifest.get("scripts", {}).get("build", [])
-    for script in build_scripts:
-        # Normalize multi-line scripts into single RUN command
-        stripped_lines = [
-            line.strip() for line in script.strip().split("\n") if line.strip()
-        ]
-        if stripped_lines:
-            normalized = " && ".join(stripped_lines)
-            lines.append(f"RUN {normalized}")
-    if build_scripts:
-        lines.append("")
-
-    # After build scripts, ensure everything in home is owned by the user
-    if user and build_scripts:
-        lines.append(f"RUN chown -R {name}:{name} {home}")
-        lines.append("")
-
-    # Create mount target directories
-    mounts = manifest.get("mounts", [])
-    if mounts:
-        dirs = [mount["target"] for mount in mounts]
-        dir_str = " ".join(dirs)
-        lines.append(f"RUN mkdir -p {dir_str}")
-        if user:
-            lines.append(f"RUN chown -R {user['name']}:{user['name']} {dir_str}")
-        lines.append("")
-
-    # Entrypoint for startup scripts
-    startup_scripts = manifest.get("scripts", {}).get("startup", [])
-    if startup_scripts:
-        lines.append(
-            "COPY .headquarter/entrypoint.sh /usr/local/bin/headquarter-entrypoint"
-        )
-        lines.append("RUN chmod +x /usr/local/bin/headquarter-entrypoint")
-        lines.append("")
-
-    # Switch to runtime user
-    if user:
-        lines.append(f"USER {user['name']}")
-        lines.append(f"WORKDIR /home/{user['name']}")
-        lines.append("")
-
-    # Entrypoint and CMD
-    runtime = manifest.get("runtime", {})
-    if startup_scripts:
-        lines.append('ENTRYPOINT ["/usr/local/bin/headquarter-entrypoint"]')
-
-    command = runtime.get("command", ["/bin/bash"])
-    cmd_json = json.dumps(command)
-    lines.append(f"CMD {cmd_json}")
-
-    return "\n".join(lines)
-
-
-def compile_entrypoint(manifest: dict) -> str:
-    """Generate the startup entrypoint script from startup scripts.
-
-    Args:
-        manifest: Fully resolved manifest JSON.
-
-    Returns:
-        Shell script content.
-    """
-    lines = ["#!/bin/bash", "set -e", ""]
-
-    startup_scripts = manifest.get("scripts", {}).get("startup", [])
-    for script in startup_scripts:
-        lines.append(script)
-        lines.append("")
-
-    lines.append('exec "$@"')
-    return "\n".join(lines)
-
-
-def compile_compose(manifest: dict, variables: dict[str, Any]) -> str:
-    """Compile a resolved manifest into a Docker Compose string.
-
-    Args:
-        manifest: Fully resolved manifest JSON.
-        variables: Resolved values: IMAGE_TAG, INSTANCE_NAME, REPO_PATH, etc.
-
-    Returns:
-        Docker Compose YAML content.
-    """
-    runtime = manifest.get("runtime", {})
-    user = manifest.get("user")
-    interface_type = manifest["interface_type"]
-
-    service: dict[str, Any] = {
-        "image": variables["IMAGE_TAG"],
-        "container_name": variables["INSTANCE_NAME"],
-        "restart": "unless-stopped",
-    }
-
-    # Terminal-specific fields
-    if runtime.get("stdin_open", False):
-        service["stdin_open"] = True
-    if runtime.get("tty", False):
-        service["tty"] = True
-    if runtime.get("working_dir"):
-        service["working_dir"] = runtime["working_dir"]
-
-    # User override
-    if user:
-        service["user"] = f"{user['uid']}:{user['gid']}"
-
-    # Ports for web tools
-    default_port = manifest.get("default_port")
-    if interface_type == "web" and default_port:
-        service["ports"] = [f"{variables['TOOL_PORT']}:{default_port}"]
-
-    # Environment
-    env = manifest.get("env", {})
-    if env:
-        service["environment"] = dict(env)
-
-    # Merge extra env from config
-    extra_env = variables.get("EXTRA_ENV", {})
-    if extra_env:
-        if "environment" not in service:
-            service["environment"] = {}
-        service["environment"].update(extra_env)
-
-    # Volumes from mount schema
-    volumes = []
-    for mount in manifest.get("mounts", []):
-        source = resolve_mount_source(mount, variables)
-        if not source:
-            continue
-        target = mount["target"]
-        readonly = ":ro" if mount.get("readonly", False) else ""
-        volumes.append(f"{source}:{target}{readonly}")
-
-    # Append extra volumes from tool config / config profile
-    for vol in variables.get("EXTRA_VOLUMES", []):
-        vol_str = f"{vol['source']}:{vol['target']}"
-        if vol.get("readonly"):
-            vol_str += ":ro"
-        volumes.append(vol_str)
-
-    if volumes:
-        service["volumes"] = sort_volumes_by_specificity(volumes)
-
-    compose = {"services": {"app": service}}
-    result = yaml.dump(compose, default_flow_style=False)
-
-    # Debug: log mount resolution so we can diagnose missing mounts
-    import logging
-    logger = logging.getLogger(__name__)
-    logger.debug(
-        "compile_compose: REPO_PATH=%s SSH_PATH=%s EXTRA_VOLUMES=%s mounts=%s volumes=%s",
-        variables.get("REPO_PATH", "<empty>"),
-        variables.get("SSH_PATH", "<empty>"),
-        variables.get("EXTRA_VOLUMES", []),
-        manifest.get("mounts", []),
-        volumes,
-    )
-
-    return result
-
-
-def resolve_mount_source(mount: dict, variables: dict[str, Any]) -> str:
-    """Resolve a mount's source_type to an actual host path.
-
-    Args:
-        mount: Mount definition from manifest.
-        variables: Resolved variables dict.
-
-    Returns:
-        Host path string, or empty string if unresolved.
-    """
-    source_type = mount.get("source_type", "host_path")
-
-    if source_type == "repo":
-        return variables.get("REPO_PATH", "")
-    elif source_type == "ssh_key":
-        return variables.get("SSH_PATH", "")
-    elif source_type == "instance":
-        instance_dir = variables.get("INSTANCE_DIR", "")
-        mount_name = mount.get("name", "unknown")
-        return f"{instance_dir}/mounts/{mount_name}"
-    elif source_type == "git_mount":
-        ref = mount.get("git_mount_ref", "default")
-        return variables.get(f"GIT_MOUNT_{ref}", "")
-    elif source_type == "host_path":
-        return mount.get("source", "")
-
-    return ""
-
-
-def get_manifest_home_dir(manifest: dict) -> str:
-    """Get the home directory for a container based on manifest user config.
-
-    Args:
-        manifest: Fully resolved manifest JSON.
-
-    Returns:
-        Home directory path (e.g., /home/user or /root).
-    """
-    user = manifest.get("user")
-    if user and user.get("name"):
-        return f"/home/{user['name']}"
-    return "/root"
-
-
-def compute_image_tag(tool_name: str, manifest: dict) -> str:
-    """Compute a deterministic image tag from manifest content.
-
-    Args:
-        tool_name: Human-readable tool name.
-        manifest: Fully resolved manifest JSON.
-
-    Returns:
-        Docker image tag string.
-    """
-    # Canonicalize: sort keys, stable JSON
-    canonical = json.dumps(manifest, sort_keys=True, separators=(",", ":"))
-    hash_suffix = hashlib.sha256(canonical.encode()).hexdigest()[:8]
-    safe_name = tool_name.lower().replace(" ", "-").replace("_", "-")
-    return f"headquarter/{safe_name}-{hash_suffix}:latest"
-
-
-def merge_with_config(manifest: dict, profile: dict | None = None) -> dict:
-    """Merge ConfigProfile overrides into a manifest.
-
-    Args:
-        manifest: Base manifest from tool definition.
-        profile: Resolved ConfigProfile (optional).
-
-    Returns:
-        Manifest with overrides applied.
-    """
-    result = deepcopy(manifest)
-
-    extra_env: dict[str, str] = {}
-    extra_volumes: list[dict] = []
-
-    # Apply ConfigProfile
-    if profile:
-        if profile.get("environment_variables"):
-            extra_env.update(profile["environment_variables"])
-        if profile.get("mounts"):
-            extra_volumes.extend(profile["mounts"])
-        # Profile hints override everything
-        hints = profile.get("hints", {})
-        if hints.get("start_command"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["command"] = hints["start_command"].split()
-        if hints.get("working_directory"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["working_dir"] = hints["working_directory"]
-        if hints.get("port_override"):
-            result["default_port"] = hints["port_override"]
-
-    # Store merged extras for the compose compiler
-    result["_extra_env"] = extra_env
-    result["_extra_volumes"] = extra_volumes
-
-    return result

apps/api/src/services/notification_service.py

@@ -1,272 +0,0 @@
-"""Notification persistence service."""
-
-import uuid
-from datetime import datetime, timezone
-from typing import Any
-
-from sqlalchemy import func, select, update
-from sqlalchemy.engine import CursorResult
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.notification import Notification
-
-
-class NotificationService:
-    """Singleton notification persistence service.
-
-    All methods filter by user_id to enforce strict ownership isolation.
-    """
-
-    async def create_notification(
-        self,
-        session: AsyncSession,
-        user_id: uuid.UUID,
-        *,
-        category: str,
-        severity: str,
-        title: str,
-        message: str | None = None,
-        source_type: str | None = None,
-        source_id: uuid.UUID | None = None,
-        metadata: dict[str, Any] | None = None,
-    ) -> Notification:
-        """Insert a new notification row.
-
-        Args:
-            session: Database session.
-            user_id: Owner of the notification.
-            category: Notification category (e.g., instance, system, health).
-            severity: Severity level (e.g., info, warning, error, success).
-            title: Short notification title.
-            message: Optional longer message body.
-            source_type: Optional source entity type.
-            source_id: Optional source entity UUID.
-            metadata: Optional JSON metadata dictionary.
-
-        Returns:
-            The newly created Notification instance.
-        """
-        notification = Notification(
-            user_id=user_id,
-            category=category,
-            severity=severity,
-            title=title,
-            message=message,
-            source_type=source_type,
-            source_id=source_id,
-            notification_metadata=metadata or {},
-        )
-        session.add(notification)
-        await session.commit()
-        await session.refresh(notification)
-        return notification
-
-    async def list_notifications(
-        self,
-        session: AsyncSession,
-        user_id: uuid.UUID,
-        *,
-        limit: int = 20,
-        offset: int = 0,
-        unread_only: bool = False,
-        mute_categories: list[str] | None = None,
-    ) -> tuple[list[Notification], int]:
-        """Return paginated notifications for a user.
-
-        Excludes dismissed notifications and applies optional filtering.
-
-        Args:
-            session: Database session.
-            user_id: Owner of the notifications.
-            limit: Maximum number of items to return.
-            offset: Number of items to skip.
-            unread_only: If True, only return unread notifications.
-            mute_categories: Categories to exclude from results.
-
-        Returns:
-            A tuple of (items, total_count).
-        """
-        where_clauses = [
-            Notification.user_id == user_id,
-            Notification.dismissed_at.is_(None),
-        ]
-
-        if unread_only:
-            where_clauses.append(Notification.read_at.is_(None))
-
-        if mute_categories:
-            where_clauses.append(Notification.category.not_in(mute_categories))
-
-        total_stmt = (
-            select(func.count()).select_from(Notification).where(*where_clauses)
-        )
-        total_result = await session.execute(total_stmt)
-        total = total_result.scalar_one()
-
-        items_stmt = (
-            select(Notification)
-            .where(*where_clauses)
-            .order_by(Notification.created_at.desc())
-            .limit(limit)
-            .offset(offset)
-        )
-        items_result = await session.execute(items_stmt)
-        items = list(items_result.scalars().all())
-
-        return items, total
-
-    async def get_unread_count(
-        self,
-        session: AsyncSession,
-        user_id: uuid.UUID,
-    ) -> int:
-        """Count unread, non-dismissed notifications for a user.
-
-        Args:
-            session: Database session.
-            user_id: Owner of the notifications.
-
-        Returns:
-            Number of unread notifications.
-        """
-        stmt = (
-            select(func.count())
-            .select_from(Notification)
-            .where(
-                Notification.user_id == user_id,
-                Notification.read_at.is_(None),
-                Notification.dismissed_at.is_(None),
-            )
-        )
-        result = await session.execute(stmt)
-        return result.scalar_one()
-
-    async def mark_read(
-        self,
-        session: AsyncSession,
-        notification_id: uuid.UUID,
-        user_id: uuid.UUID,
-    ) -> Notification:
-        """Mark a single notification as read.
-
-        Args:
-            session: Database session.
-            notification_id: UUID of the notification to mark.
-            user_id: Owner of the notification.
-
-        Returns:
-            The updated Notification instance.
-
-        Raises:
-            ValueError: If the notification does not exist or is not owned by the user.
-        """
-        notification = await self._get_owned_notification(
-            session, notification_id, user_id
-        )
-        notification.read_at = datetime.now(timezone.utc)
-        await session.commit()
-        await session.refresh(notification)
-        return notification
-
-    async def mark_all_read(
-        self,
-        session: AsyncSession,
-        user_id: uuid.UUID,
-    ) -> int:
-        """Mark all unread notifications as read for a user.
-
-        Args:
-            session: Database session.
-            user_id: Owner of the notifications.
-
-        Returns:
-            Number of rows updated.
-        """
-        stmt = (
-            update(Notification)
-            .where(
-                Notification.user_id == user_id,
-                Notification.read_at.is_(None),
-                Notification.dismissed_at.is_(None),
-            )
-            .values(read_at=datetime.now(timezone.utc))
-        )
-        result: CursorResult[Any] = await session.execute(stmt)  # type: ignore[assignment]
-        await session.commit()
-        return result.rowcount or 0
-
-    async def dismiss_all(
-        self,
-        session: AsyncSession,
-        user_id: uuid.UUID,
-    ) -> int:
-        """Soft-delete all non-dismissed notifications for a user.
-
-        Args:
-            session: Database session.
-            user_id: Owner of the notifications.
-
-        Returns:
-            Number of rows updated.
-        """
-        stmt = (
-            update(Notification)
-            .where(
-                Notification.user_id == user_id,
-                Notification.dismissed_at.is_(None),
-            )
-            .values(dismissed_at=datetime.now(timezone.utc))
-        )
-        result: CursorResult[Any] = await session.execute(stmt)  # type: ignore[assignment]
-        await session.commit()
-        return result.rowcount or 0
-
-    async def dismiss(
-        self,
-        session: AsyncSession,
-        notification_id: uuid.UUID,
-        user_id: uuid.UUID,
-    ) -> None:
-        """Soft-delete a notification by setting dismissed_at.
-
-        Args:
-            session: Database session.
-            notification_id: UUID of the notification to dismiss.
-            user_id: Owner of the notification.
-
-        Raises:
-            ValueError: If the notification does not exist or is not owned by the user.
-        """
-        notification = await self._get_owned_notification(
-            session, notification_id, user_id
-        )
-        notification.dismissed_at = datetime.now(timezone.utc)
-        await session.commit()
-
-    async def _get_owned_notification(
-        self,
-        session: AsyncSession,
-        notification_id: uuid.UUID,
-        user_id: uuid.UUID,
-    ) -> Notification:
-        """Fetch a notification and verify ownership.
-
-        Args:
-            session: Database session.
-            notification_id: UUID of the notification.
-            user_id: Expected owner.
-
-        Returns:
-            The Notification instance.
-
-        Raises:
-            ValueError: If the notification does not exist or is not owned.
-        """
-        notification = await session.get(Notification, notification_id)
-        if notification is None or notification.user_id != user_id:
-            raise ValueError("Notification not found")
-        return notification
-
-
-# Module-level singleton instance
-notification_service = NotificationService()

apps/api/src/services/permission_fixer.py

@@ -1,310 +0,0 @@
-"""Permission fixer: applies mount permission policies post-start."""
-
-import logging
-import subprocess
-from typing import Any
-
-logger = logging.getLogger(__name__)
-
-
-def apply_mount_permissions(
-    container_id: str,
-    mounts: list[dict],
-    timeout: int = 10,
-) -> list[dict[str, Any]]:
-    """Apply permission policies to mounted directories in a running container.
-
-    Runs `chown`, `chmod`, and file-mode fixes for each mount that declares
-    an owner, mode, or file_mode. Requires the container to have a root user.
-
-    Args:
-        container_id: Docker container ID or name.
-        mounts: List of mount definitions from the manifest.
-        timeout: Max seconds per docker exec command.
-
-    Returns:
-        List of result dicts: [{mount_name, success, error}]
-    """
-    results = []
-
-    for mount in mounts:
-        name = mount.get("name", "unknown")
-        target = mount["target"]
-        owner = mount.get("owner")
-        mode = mount.get("mode")
-        file_mode = mount.get("file_mode")
-
-        result: dict[str, Any] = {
-            "mount_name": name,
-            "success": True,
-            "error": None,
-        }
-
-        # Skip read-only mounts — their permissions cannot be changed
-        # post-start because the bind mount is locked.
-        if mount.get("readonly", False):
-            logger.debug(
-                "Skipping permission fix for read-only mount %s (target=%s)",
-                name,
-                target,
-            )
-            results.append(result)
-            continue
-
-        # Skip if no permission policy defined
-        if not owner and not mode and not file_mode:
-            results.append(result)
-            continue
-
-        try:
-            if owner:
-                _run_in_container(
-                    container_id,
-                    ["chown", "-R", f"{owner}:{owner}", target],
-                    timeout,
-                )
-                logger.debug(
-                    "Applied owner %s to %s in container %s",
-                    owner,
-                    target,
-                    container_id,
-                )
-
-            if mode and result["success"]:
-                _run_in_container(
-                    container_id,
-                    ["chmod", mode, target],
-                    timeout,
-                )
-                logger.debug(
-                    "Applied mode %s to %s in container %s",
-                    mode,
-                    target,
-                    container_id,
-                )
-
-            if file_mode and result["success"]:
-                _run_in_container(
-                    container_id,
-                    [
-                        "sh",
-                        "-c",
-                        f"find {target} -type f -exec chmod {file_mode} {{}} +",
-                    ],
-                    timeout,
-                )
-                logger.debug(
-                    "Applied file_mode %s to files in %s in container %s",
-                    file_mode,
-                    target,
-                    container_id,
-                )
-
-        except PermissionFixError as exc:
-            result["success"] = False
-            result["error"] = str(exc)
-            logger.warning(
-                "Permission fix failed for mount %s (target=%s): %s",
-                name,
-                target,
-                exc,
-            )
-
-        results.append(result)
-
-    return results
-
-
-def _exec_and_log(
-    container_id: str,
-    command: list[str],
-    timeout: int,
-    description: str,
-) -> str:
-    """Run a docker exec command and log stdout/stderr for debugging."""
-    cmd = ["docker", "exec", "--user", "root", container_id] + command
-    logger.debug("[SSH-fix] %s: %s", description, " ".join(cmd))
-
-    try:
-        result = subprocess.run(
-            cmd,
-            capture_output=True,
-            text=True,
-            timeout=timeout,
-        )
-    except subprocess.TimeoutExpired:
-        raise PermissionFixError(
-            f"Command timed out after {timeout}s: {' '.join(command)}"
-        )
-    except FileNotFoundError:
-        raise PermissionFixError(f"Docker command not found: {' '.join(command)}")
-
-    stdout = result.stdout.strip()
-    stderr = result.stderr.strip()
-    if stdout:
-        logger.debug("[SSH-fix] %s stdout: %s", description, stdout)
-    if stderr:
-        logger.debug("[SSH-fix] %s stderr: %s", description, stderr)
-
-    if result.returncode != 0:
-        raise PermissionFixError(
-            f"Command failed (rc={result.returncode}): {stderr or '(no stderr)'}"
-        )
-    return stdout
-
-
-def apply_ssh_permissions(
-    container_id: str,
-    ssh_target: str,
-    container_user: str,
-    timeout: int = 10,
-) -> dict[str, Any]:
-    """Fix SSH directory ownership and permissions in a running container.
-
-    Runs chown and chmod on the ~/.ssh directory so the container user
-    can use the keys (SSH requires the private key to be owned by the
-    user with mode 600).
-
-    Args:
-        container_id: Docker container ID or name.
-        ssh_target: Absolute path to the .ssh directory inside the container.
-        container_user: The container user that should own the keys.
-        timeout: Max seconds per docker exec command.
-
-    Returns:
-        Result dict with keys: success, error.
-    """
-    result: dict[str, Any] = {"success": True, "error": None}
-    try:
-        # 1. Ensure directory is owned by the container user
-        _exec_and_log(
-            container_id,
-            ["chown", "-R", f"{container_user}:{container_user}", ssh_target],
-            timeout,
-            "chown",
-        )
-
-        # 2. Set directory permissions
-        _exec_and_log(
-            container_id,
-            ["chmod", "700", ssh_target],
-            timeout,
-            "chmod-dir",
-        )
-
-        # 3. Set private key permissions (id_ed25519, id_rsa, etc.)
-        _exec_and_log(
-            container_id,
-            [
-                "sh",
-                "-c",
-                f"find {ssh_target} -name 'id_*' -type f -exec chmod 600 {{}} +",
-            ],
-            timeout,
-            "chmod-keys",
-        )
-
-        # 4. Verify final state
-        ls_output = _exec_and_log(
-            container_id,
-            ["ls", "-la", ssh_target],
-            timeout,
-            "verify-ls",
-        )
-        stat_output = _exec_and_log(
-            container_id,
-            ["stat", "-c", "%U:%G %a %n", ssh_target],
-            timeout,
-            "verify-stat-dir",
-        )
-        key_stat = _exec_and_log(
-            container_id,
-            [
-                "sh",
-                "-c",
-                f"stat -c '%U:%G %a %n' {ssh_target}/id_* 2>/dev/null || echo 'no id_* files found'",
-            ],
-            timeout,
-            "verify-stat-keys",
-        )
-
-        logger.info(
-            "SSH permissions fixed for container %s (user=%s, target=%s). "
-            "ls:\n%s\nstat-dir: %s\nstat-keys: %s",
-            container_id,
-            container_user,
-            ssh_target,
-            ls_output,
-            stat_output,
-            key_stat,
-        )
-    except PermissionFixError as exc:
-        result["success"] = False
-        result["error"] = str(exc)
-        logger.warning(
-            "SSH permission fix failed for container %s (target=%s): %s",
-            container_id,
-            ssh_target,
-            exc,
-        )
-    return result
-
-
-class PermissionFixError(Exception):
-    """Raised when a permission fix command fails."""
-
-    pass
-
-
-def _run_in_container(
-    container_id: str,
-    command: list[str],
-    timeout: int,
-) -> None:
-    """Run a command inside a container as root.
-
-    Args:
-        container_id: Docker container ID or name.
-        command: Command + args to execute.
-        timeout: Max seconds to wait.
-
-    Raises:
-        PermissionFixError: If the command fails or times out.
-    """
-    cmd = ["docker", "exec", "--user", "root", container_id] + command
-
-    try:
-        result = subprocess.run(
-            cmd,
-            capture_output=True,
-            text=True,
-            timeout=timeout,
-        )
-    except subprocess.TimeoutExpired:
-        raise PermissionFixError(
-            f"Command timed out after {timeout}s: {' '.join(command)}"
-        )
-    except FileNotFoundError:
-        raise PermissionFixError(f"Docker command not found: {' '.join(command)}")
-
-    if result.returncode != 0:
-        raise PermissionFixError(
-            f"Command failed (rc={result.returncode}): {result.stderr.strip()}"
-        )
-
-
-def check_root_user_available(container_id: str, timeout: int = 5) -> bool:
-    """Check if the container has a root user we can exec as.
-
-    Args:
-        container_id: Docker container ID or name.
-        timeout: Max seconds to wait.
-
-    Returns:
-        True if root user exists and is usable.
-    """
-    try:
-        _run_in_container(container_id, ["id", "root"], timeout)
-        return True
-    except PermissionFixError:
-        return False

apps/api/src/services/ssh_keys.py

@@ -1,182 +0,0 @@
-"""SSH key service utilities for preparing keys for container use."""
-
-import logging
-import os
-import re
-from pathlib import Path
-
-from cryptography.fernet import Fernet
-
-from src.config import Settings
-
-logger = logging.getLogger(__name__)
-
-
-def _get_fernet() -> Fernet:
-    """Generate a valid Fernet key from the session secret."""
-    import base64
-    import hashlib
-
-    settings = Settings()
-    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
-    key = base64.urlsafe_b64encode(key_bytes)
-    return Fernet(key)
-
-
-def _sanitize_filename(name: str) -> str:
-    """Sanitize a string for use as a filename.
-
-    Replaces non-alphanumeric characters with underscores and strips
-    leading/trailing underscores.
-    """
-    sanitized = re.sub(r"[^a-zA-Z0-9_-]", "_", name)
-    sanitized = sanitized.strip("_")
-    # Ensure it's not empty
-    if not sanitized:
-        sanitized = "key"
-    return sanitized
-
-
-def prepare_ssh_key_files(
-    instance_dir: str,
-    ssh_key,
-    subdir: str = ".ssh",
-    uid: int | None = None,
-    gid: int | None = None,
-    key_filename: str = "id_ed25519",
-    write_config: bool = True,
-) -> str:
-    """Decrypt and write SSH key files to instance directory for container mounting.
-
-    Args:
-        instance_dir: Path to instance directory
-        ssh_key: SSHKey model instance with encrypted private key
-        subdir: Subdirectory within instance_dir to write to (default: ".ssh")
-        uid: Optional UID to own the files (for bind-mount into non-root container)
-        gid: Optional GID to own the files
-        key_filename: Base filename for the key pair (default: "id_ed25519").
-            The private key will be named "{key_filename}" and the public key
-            "{key_filename}.pub".
-        write_config: Whether to write an SSH config file (default: True).
-            Set to False when combining multiple keys into one directory,
-            then call write_ssh_config() separately.
-
-    Returns:
-        Path to the .ssh directory
-    """
-    ssh_dir = Path(instance_dir) / subdir
-    ssh_dir.mkdir(parents=True, exist_ok=True)
-
-    # Decrypt private key
-    fernet = _get_fernet()
-    private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
-
-    # Write private key with restricted permissions
-    private_key_path = ssh_dir / key_filename
-    private_key_path.write_text(private_key)
-    os.chmod(private_key_path, 0o600)
-
-    # Write public key
-    public_key_path = ssh_dir / f"{key_filename}.pub"
-    public_key_path.write_text(ssh_key.public_key)
-    os.chmod(public_key_path, 0o644)
-
-    # Write SSH config (only if requested)
-    if write_config:
-        config_path = ssh_dir / "config"
-        config_content = f"""Host *
-    StrictHostKeyChecking no
-    UserKnownHostsFile /dev/null
-    IdentityFile ~/.ssh/{key_filename}
-    IdentitiesOnly yes
-"""
-        config_path.write_text(config_content)
-        os.chmod(config_path, 0o644)
-
-        # Set ownership to target container user if requested
-        if uid is not None or gid is not None:
-            effective_uid = uid if uid is not None else -1
-            effective_gid = gid if gid is not None else -1
-            try:
-                os.chown(ssh_dir, effective_uid, effective_gid)
-                os.chown(private_key_path, effective_uid, effective_gid)
-                os.chown(public_key_path, effective_uid, effective_gid)
-                os.chown(config_path, effective_uid, effective_gid)
-                logger.debug(
-                    "Set SSH key ownership to uid=%s gid=%s for %s",
-                    effective_uid,
-                    effective_gid,
-                    ssh_dir,
-                )
-            except PermissionError as exc:
-                logger.warning(
-                    "Cannot chown SSH keys to uid=%s gid=%s (running as uid=%s): %s",
-                    effective_uid,
-                    effective_gid,
-                    os.getuid(),
-                    exc,
-                )
-    else:
-        # Still chown the key files even if we didn't write config
-        if uid is not None or gid is not None:
-            effective_uid = uid if uid is not None else -1
-            effective_gid = gid if gid is not None else -1
-            try:
-                os.chown(private_key_path, effective_uid, effective_gid)
-                os.chown(public_key_path, effective_uid, effective_gid)
-            except PermissionError:
-                pass
-
-    return str(ssh_dir)
-
-
-def write_ssh_config(
-    ssh_dir: str,
-    key_filenames: list[str],
-    uid: int | None = None,
-    gid: int | None = None,
-) -> None:
-    """Write an SSH config file that includes multiple IdentityFile entries.
-
-    Args:
-        ssh_dir: Path to the .ssh directory
-        key_filenames: List of key filenames (without .pub extension)
-        uid: Optional UID to own the config file
-        gid: Optional GID to own the config file
-    """
-    ssh_dir_path = Path(ssh_dir)
-    ssh_dir_path.mkdir(parents=True, exist_ok=True)
-
-    config_path = ssh_dir_path / "config"
-    lines = ["Host *"]
-    lines.append("    StrictHostKeyChecking no")
-    lines.append("    UserKnownHostsFile /dev/null")
-    lines.append("    IdentitiesOnly yes")
-    for filename in key_filenames:
-        lines.append(f"    IdentityFile ~/.ssh/{filename}")
-    lines.append("")
-
-    config_content = "\n".join(lines)
-    config_path.write_text(config_content)
-    os.chmod(config_path, 0o644)
-
-    if uid is not None or gid is not None:
-        effective_uid = uid if uid is not None else -1
-        effective_gid = gid if gid is not None else -1
-        try:
-            os.chown(config_path, effective_uid, effective_gid)
-        except PermissionError:
-            pass
-
-
-def cleanup_ssh_key_files(instance_dir: str) -> None:
-    """Remove temporary SSH key files from instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-    """
-    ssh_dir = Path(instance_dir) / ".ssh"
-    if ssh_dir.exists():
-        for file_path in ssh_dir.iterdir():
-            file_path.unlink()
-        ssh_dir.rmdir()

apps/api/src/services/tunnel.py

@@ -1,281 +0,0 @@
-"""Clean tunnel service using cloudflared containers on the backend network.
-
-Design:
-- Each tunnel runs as a Docker container on the same 'backend' network as the API.
-- cloudflared connects to the tool container by its Docker Compose service name
-  (e.g. http://code-server-headquarter-34837cd3:8443).
-- This avoids host port conflicts and DNS resolution issues.
-"""
-
-import logging
-import re
-import subprocess
-from typing import Any
-
-from src.services.docker import get_backend_network_name
-
-logger = logging.getLogger(__name__)
-
-TUNNEL_IMAGE = "cloudflare/cloudflared:latest"
-
-
-def _tunnel_container_name(instance_name: str) -> str:
-    return f"tunnel-{instance_name.lower()}"
-
-
-def _ensure_image() -> None:
-    """Pull cloudflared image if not already present."""
-    result = subprocess.run(
-        ["docker", "images", "-q", TUNNEL_IMAGE],
-        capture_output=True,
-        text=True,
-    )
-    if not result.stdout.strip():
-        logger.info("Pulling %s ...", TUNNEL_IMAGE)
-        pull = subprocess.run(
-            ["docker", "pull", TUNNEL_IMAGE],
-            capture_output=True,
-            text=True,
-        )
-        if pull.returncode != 0:
-            logger.warning("Failed to pull %s: %s", TUNNEL_IMAGE, pull.stderr)
-
-
-def _cleanup_stale_tunnel(tunnel_name: str) -> None:
-    """Remove any existing tunnel container with this name."""
-    subprocess.run(
-        ["docker", "stop", "-t", "3", tunnel_name],
-        capture_output=True,
-        text=True,
-    )
-    subprocess.run(
-        ["docker", "rm", "-f", tunnel_name],
-        capture_output=True,
-        text=True,
-    )
-
-
-def _get_container_logs(tunnel_name: str) -> tuple[str, str]:
-    """Get stdout and stderr logs from a container."""
-    result = subprocess.run(
-        ["docker", "logs", tunnel_name],
-        capture_output=True,
-        text=True,
-    )
-    return result.stdout, result.stderr
-
-
-def _get_container_exit_code(tunnel_name: str) -> int | None:
-    """Get exit code of a container if it has exited."""
-    result = subprocess.run(
-        ["docker", "inspect", "-f", "{{.State.ExitCode}}", tunnel_name],
-        capture_output=True,
-        text=True,
-    )
-    if result.returncode == 0:
-        try:
-            return int(result.stdout.strip())
-        except ValueError:
-            pass
-    return None
-
-
-def start_tunnel(
-    instance_name: str,
-    container_port: int,
-    timeout: int = 30,
-    target_url: str | None = None,
-) -> dict[str, str]:
-    """Start a temporary Cloudflare tunnel for an instance.
-
-    Args:
-        instance_name: The tool instance name (used for tunnel naming).
-        container_port: The port the tool container listens on internally.
-        timeout: Seconds to wait for the tunnel URL.
-        target_url: Optional explicit URL to proxy to. If omitted, derives
-            http://{instance_name.lower()}:{container_port}.
-
-    Returns:
-        Dict with 'url' and 'container_name'.
-    """
-    _ensure_image()
-
-    tunnel_name = _tunnel_container_name(instance_name)
-    _cleanup_stale_tunnel(tunnel_name)
-
-    # Target the tool container by name on the backend network
-    if target_url is None:
-        target_url = f"http://{instance_name.lower()}:{container_port}"
-
-    cmd = [
-        "docker",
-        "run",
-        "-d",
-        "--network",
-        get_backend_network_name(),
-        "--name",
-        tunnel_name,
-        TUNNEL_IMAGE,
-        "tunnel",
-        "--no-autoupdate",
-        "--url",
-        target_url,
-    ]
-
-    logger.debug("Running: %s", " ".join(cmd))
-    proc = subprocess.run(cmd, capture_output=True, text=True)
-    if proc.returncode != 0:
-        raise RuntimeError(
-            f"Failed to start tunnel container {tunnel_name}: {proc.stderr}"
-        )
-
-    container_id = proc.stdout.strip()
-    logger.debug("Tunnel container started: %s", container_id)
-
-    # Wait for URL to appear in logs
-    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
-    start_time = __import__("time").time()
-    url: str | None = None
-    combined_logs = ""
-
-    while __import__("time").time() - start_time < timeout:
-        stdout, stderr = _get_container_logs(tunnel_name)
-        combined_logs = stdout + "\n" + stderr
-
-        match = url_pattern.search(combined_logs)
-        if match:
-            url = match.group(0)
-            break
-
-        # Check if container exited early
-        exit_code = _get_container_exit_code(tunnel_name)
-        if exit_code is not None and exit_code != 0:
-            _cleanup_stale_tunnel(tunnel_name)
-            raise RuntimeError(
-                f"Tunnel container {tunnel_name} exited with code {exit_code}. "
-                f"Logs:\n{combined_logs[-3000:]}"
-            )
-
-        __import__("time").sleep(0.5)
-
-    if not url:
-        stdout, stderr = _get_container_logs(tunnel_name)
-        combined_logs = stdout + "\n" + stderr
-        exit_code = _get_container_exit_code(tunnel_name)
-
-        _cleanup_stale_tunnel(tunnel_name)
-        raise RuntimeError(
-            f"Tunnel {tunnel_name} did not produce a URL within {timeout}s. "
-            f"Exit code: {exit_code}. Logs:\n{combined_logs[-3000:]}"
-        )
-
-    # Wait a moment for Cloudflare DNS edge to propagate the new tunnel subdomain
-    __import__("time").sleep(2)
-
-    logger.info(
-        "Tunnel %s started for %s → %s (%s)",
-        tunnel_name,
-        instance_name,
-        target_url,
-        url,
-    )
-    return {"url": url, "container_name": tunnel_name}
-
-
-def stop_tunnel(instance_name: str) -> None:
-    """Stop and remove the tunnel container for an instance."""
-    tunnel_name = _tunnel_container_name(instance_name)
-    _cleanup_stale_tunnel(tunnel_name)
-    logger.debug("Stopped and removed tunnel container %s", tunnel_name)
-
-
-def recreate_tunnel(
-    instance_name: str, container_port: int, target_url: str | None = None
-) -> dict[str, str]:
-    """Recreate a tunnel for an instance.
-
-    Args:
-        instance_name: The tool instance name.
-        container_port: The port the tool container listens on internally.
-        target_url: Optional explicit origin URL. If omitted, derives
-            http://{instance_name.lower()}:{container_port}.
-    """
-    stop_tunnel(instance_name)
-    return start_tunnel(instance_name, container_port, target_url=target_url)
-
-
-def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
-    """Check if a tunnel URL is healthy.
-
-    Returns:
-        Dict with 'tunnel_status', 'status_code', 'healthy', 'error'.
-    """
-    try:
-        result = subprocess.run(
-            [
-                "curl",
-                "-s",
-                "-o",
-                "/dev/null",
-                "-w",
-                "%{http_code}",
-                "--max-time",
-                str(timeout),
-                url,
-            ],
-            capture_output=True,
-            text=True,
-            timeout=timeout + 5,
-        )
-        status_code = int(result.stdout.strip())
-
-        if 200 <= status_code < 400:
-            return {
-                "tunnel_status": "healthy",
-                "status_code": status_code,
-                "healthy": True,
-                "error": None,
-            }
-        if status_code in (502, 503, 504):
-            return {
-                "tunnel_status": "error_response",
-                "status_code": status_code,
-                "healthy": False,
-                "error": f"Application returned HTTP {status_code}",
-            }
-        return {
-            "tunnel_status": "error_response",
-            "status_code": status_code,
-            "healthy": False,
-            "error": f"HTTP {status_code}",
-        }
-    except subprocess.TimeoutExpired:
-        return {
-            "tunnel_status": "unreachable",
-            "status_code": None,
-            "healthy": False,
-            "error": "Tunnel request timed out",
-        }
-    except (ValueError, Exception) as exc:
-        error_str = str(exc).lower()
-        if any(
-            err in error_str
-            for err in [
-                "connection refused",
-                "econnrefused",
-                "could not resolve",
-                "nodename",
-            ]
-        ):
-            return {
-                "tunnel_status": "unreachable",
-                "status_code": None,
-                "healthy": False,
-                "error": f"Tunnel unreachable: {exc}",
-            }
-        return {
-            "tunnel_status": "unreachable",
-            "status_code": None,
-            "healthy": False,
-            "error": str(exc),
-        }

apps/api/src/services/workspace_manager.py

@@ -1,257 +0,0 @@
-"""Workspace lifecycle management service."""
-
-from __future__ import annotations
-
-import contextlib
-import logging
-import os
-import shutil
-import stat
-import uuid
-from dataclasses import dataclass
-from datetime import datetime
-from typing import TYPE_CHECKING
-
-from sqlalchemy import select
-
-from src.models.workspace import Workspace
-from src.services.git_service import GitService
-from src.services.ssh_keys import _get_fernet
-
-if TYPE_CHECKING:
-    from sqlalchemy.ext.asyncio import AsyncSession
-
-    from src.models.git_repository import GitRepository
-    from src.models.tool_instance import ToolInstance
-
-logger = logging.getLogger(__name__)
-
-
-@dataclass
-class SyncResult:
-    """Result of a workspace sync operation."""
-
-    branch_deleted: bool = False
-
-
-class WorkspaceHasInstancesError(Exception):
-    """Raised when attempting to delete a workspace with running instances."""
-
-    def __init__(self, instances: list[dict]) -> None:
-        self.instances = instances
-        super().__init__(f"Workspace has {len(instances)} running tool instance(s)")
-
-
-class WorkspaceManager:
-    """Manages workspace lifecycle: create, delete, sync, validate."""
-
-    BASE_PATH = "/data/working-copies"
-
-    def _workspace_path(self, repo_id: uuid.UUID, name: str) -> str:
-        """Return the filesystem path for a workspace."""
-        return os.path.join(self.BASE_PATH, str(repo_id), name)
-
-    async def create(
-        self,
-        repo: GitRepository,
-        user_id: uuid.UUID,
-        name: str,
-        branch: str = "main",
-        session: AsyncSession | None = None,
-    ) -> Workspace:
-        """Clone repo to workspace path and create DB record.
-
-        Args:
-            repo: The git repository to clone.
-            user_id: The owner user ID.
-            name: The workspace name (unique per repo).
-            branch: The branch to clone (default: "main").
-            session: Database session for loading SSH keys.
-
-        Returns:
-            The created Workspace record.
-
-        Raises:
-            RuntimeError: If git clone fails.
-        """
-        path = self._workspace_path(repo.id, name)
-        parent = os.path.dirname(path)
-        os.makedirs(parent, exist_ok=True)
-        # Ensure container users (various UIDs) can write to workspace dirs
-        with contextlib.suppress(OSError):
-            os.chmod(parent, 0o777)
-
-        logger.info(
-            "Creating workspace: name=%s, repo=%s, branch=%s", name, repo.id, branch
-        )
-
-        if not repo.remote_url:
-            raise ValueError("Repository has no remote URL")
-
-        # Remove stale directory from previous failed/aborted clone
-        if os.path.exists(path):
-            logger.warning("Removing stale workspace directory: %s", path)
-            shutil.rmtree(path, ignore_errors=True)
-
-        # Load SSH key if repo has one
-        ssh_key = None
-        if getattr(repo, "ssh_key_id", None) and session is not None:
-            from src.models.ssh_key import SSHKey
-
-            result = await session.execute(
-                select(SSHKey).where(SSHKey.id == repo.ssh_key_id)
-            )
-            ssh_key_obj = result.scalar_one_or_none()
-            if ssh_key_obj:
-                fernet = _get_fernet()
-                ssh_key = fernet.decrypt(
-                    ssh_key_obj.private_key_encrypted.encode()
-                ).decode()
-
-        await GitService.clone(repo.remote_url, branch, path, ssh_key=ssh_key)
-        self._make_world_writable(path)
-
-        workspace = Workspace(
-            name=name,
-            repo_id=repo.id,
-            user_id=user_id,
-            branch=branch,
-            path=path,
-            status="ready",
-            last_sync_at=datetime.now(),
-        )
-        logger.info("Workspace created: %s", workspace.id)
-        return workspace
-
-    async def delete(
-        self,
-        workspace: Workspace,
-        force: bool = False,
-        session: AsyncSession | None = None,
-    ) -> None:
-        """Delete a workspace and all associated tool instances.
-
-        Args:
-            workspace: The workspace to delete.
-            force: If True, delete even if instances exist.
-            session: The database session (required for checking instances).
-
-        Raises:
-            WorkspaceHasInstancesError: If instances exist and force=False.
-        """
-        if session is None:
-            raise ValueError("session is required for delete")
-
-        instances = await self._get_instances(workspace, session)
-        if instances and not force:
-            raise WorkspaceHasInstancesError(
-                [{"id": str(i.id), "name": i.name} for i in instances]
-            )
-
-        # Stop and delete all instances
-        for instance in instances:
-            await self._stop_and_delete_instance(instance)
-
-        # Delete directory
-        if os.path.exists(workspace.path):
-            shutil.rmtree(workspace.path, ignore_errors=True)
-            logger.info("Deleted workspace directory: %s", workspace.path)
-
-        # Delete record
-        await session.delete(workspace)
-        logger.info("Deleted workspace record: %s", workspace.id)
-
-    async def sync(
-        self, workspace: Workspace, session: AsyncSession | None = None
-    ) -> SyncResult:
-        """Sync a workspace with its remote.
-
-        Args:
-            workspace: The workspace to sync.
-            session: Database session for loading SSH keys.
-
-        Returns:
-            SyncResult indicating whether the branch was deleted.
-
-        Raises:
-            RuntimeError: If git operations fail.
-        """
-        logger.info("Syncing workspace: %s", workspace.id)
-
-        # Load SSH key if repo has one
-        ssh_key = None
-        if session is not None:
-            from src.models.git_repository import GitRepository
-            from src.models.ssh_key import SSHKey
-
-            repo = await session.get(GitRepository, workspace.repo_id)
-            if repo and getattr(repo, "ssh_key_id", None):
-                result = await session.execute(
-                    select(SSHKey).where(SSHKey.id == repo.ssh_key_id)
-                )
-                ssh_key_obj = result.scalar_one_or_none()
-                if ssh_key_obj:
-                    fernet = _get_fernet()
-                    ssh_key = fernet.decrypt(
-                        ssh_key_obj.private_key_encrypted.encode()
-                    ).decode()
-
-        await GitService.fetch(workspace.path, ssh_key=ssh_key)
-
-        if not GitService.branch_exists_remotely(
-            workspace.path, workspace.branch, ssh_key=ssh_key
-        ):
-            return SyncResult(branch_deleted=True)
-
-        await GitService.pull(workspace.path, workspace.branch, ssh_key=ssh_key)
-        self._make_world_writable(workspace.path)
-
-        workspace.last_sync_at = datetime.now()
-        logger.info("Workspace synced: %s", workspace.id)
-        return SyncResult(branch_deleted=False)
-
-    def _make_world_writable(self, path: str) -> None:
-        """Recursively make path readable/writable/traversable by any UID.
-
-        Directories get 777 (traversable). Files get rw for all while
-        preserving any existing execute bits.
-        """
-        with contextlib.suppress(OSError):
-            os.chmod(path, 0o777)
-        for root, dirs, files in os.walk(path):
-            for d in dirs:
-                dpath = os.path.join(root, d)
-                with contextlib.suppress(OSError):
-                    os.chmod(dpath, 0o777)
-            for f in files:
-                fpath = os.path.join(root, f)
-                with contextlib.suppress(OSError):
-                    mode = os.stat(fpath).st_mode
-                    # Preserve execute bits, ensure read+write for all
-                    new_mode = (mode & stat.S_IXUSR) | 0o666
-                    if mode & stat.S_IXGRP:
-                        new_mode |= stat.S_IXGRP
-                    if mode & stat.S_IXOTH:
-                        new_mode |= stat.S_IXOTH
-                    os.chmod(fpath, new_mode)
-
-    async def _get_instances(
-        self,
-        workspace: Workspace,
-        session: AsyncSession,
-    ) -> list[ToolInstance]:
-        """Get all tool instances associated with this workspace."""
-        from src.models.tool_instance import ToolInstance
-
-        result = await session.execute(
-            select(ToolInstance).where(ToolInstance.workspace_id == workspace.id)
-        )
-        return list(result.scalars().all())
-
-    async def _stop_and_delete_instance(self, instance: ToolInstance) -> None:
-        """Stop and delete a tool instance.
-
-        TODO(PR-2): Wire up to actual instance stop/delete logic.
-        For now, this is a placeholder.
-        """
-        logger.warning("Placeholder: stopping and deleting instance %s", instance.id)

apps/api/tests/api/test_terminal_ws_multi.py

@@ -1,67 +0,0 @@
-"""Integration tests for multi-session terminal WebSocket and REST API."""
-
-import pytest
-from fastapi.testclient import TestClient
-from src.main import app
-
-
-@pytest.fixture
-def client():
-    return TestClient(app)
-
-
-class TestTerminalWebSocketMultiSession:
-    """Tests for multi-session WebSocket routing."""
-
-    def test_specific_session_websocket_route_exists(self, client):
-        """The specific session WebSocket route should be registered."""
-        # We can't easily test WebSocket without auth, but we can verify
-        # the route exists by checking for a 403 (no auth cookie)
-        response = client.get("/ws/tool-instances/test-instance/terminal/test-session")
-        # WebSocket endpoint returns 403 when accessed via HTTP GET
-        assert response.status_code in (403, 404)
-
-    def test_default_session_alias_route_exists(self, client):
-        """The default session alias route should still exist."""
-        response = client.get("/ws/tool-instances/test-instance/terminal")
-        assert response.status_code in (403, 404)
-
-
-class TestTerminalRestApi:
-    """Tests for REST API endpoints."""
-
-    def test_list_sessions_requires_auth(self, client):
-        """List sessions endpoint requires authentication."""
-        response = client.get("/instances/test/terminal/sessions")
-        assert response.status_code == 401
-
-    def test_create_session_requires_auth(self, client):
-        """Create session endpoint requires authentication."""
-        response = client.post(
-            "/instances/test/terminal/sessions",
-            json={},
-        )
-        assert response.status_code == 401
-
-    def test_close_session_requires_auth(self, client):
-        """Close session endpoint requires authentication."""
-        response = client.delete("/instances/test/terminal/sessions/test-session")
-        assert response.status_code == 401
-
-    def test_reset_session_requires_auth(self, client):
-        """Reset session endpoint requires authentication."""
-        response = client.post("/instances/test/terminal/sessions/test-session/reset")
-        assert response.status_code == 401
-
-    def test_rename_session_requires_auth(self, client):
-        """Rename session endpoint requires authentication."""
-        response = client.post(
-            "/instances/test/terminal/sessions/test-session/rename",
-            json={"name": "New Name"},
-        )
-        assert response.status_code == 401
-
-    def test_legacy_reset_alias_requires_auth(self, client):
-        """Legacy reset endpoint still requires auth."""
-        response = client.post("/instances/test/terminal/reset")
-        assert response.status_code == 401

apps/api/tests/integration/test_events.py

@@ -1,268 +0,0 @@
-"""Integration tests for SSE endpoint and lifecycle event flow."""
-
-import asyncio
-import uuid
-from collections.abc import Generator
-from typing import Any
-
-import pytest
-from fastapi.testclient import TestClient
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.api import events as events_module
-from src.auth.session import decode_session_cookie
-from src.config import Settings
-from src.models.git_repository import GitRepository
-from src.models.instance_event import InstanceEvent
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-
-
-@pytest.fixture
-def event_bus() -> Generator[InstanceEventBus, None, None]:
-    bus = InstanceEventBus()
-    bus._reset_for_testing()
-    yield bus
-    bus._reset_for_testing()
-
-
-@pytest.fixture
-def sample_payload() -> InstanceEventPayload:
-    return {
-        "event": "instance.started",
-        "instance_id": str(uuid.uuid4()),
-        "status": "starting",
-        "message": "Container starting...",
-        "metadata": {},
-        "timestamp": "2026-05-28T12:00:00Z",
-        "correlation_id": str(uuid.uuid4()),
-    }
-
-
-def _get_user_id_from_client(client: TestClient) -> uuid.UUID | None:
-    settings = Settings()
-    cookie = client.cookies.get("session")
-    if not cookie:
-        return None
-    session = decode_session_cookie(settings=settings, cookie_value=cookie)
-    if session and "user_id" in session:
-        return uuid.UUID(session["user_id"])
-    return None
-
-
-@pytest.mark.integration
-def test_sse_requires_auth(test_client: TestClient) -> None:
-    response = test_client.get("/events/stream")
-    assert response.status_code == 401
-
-
-@pytest.mark.integration
-def test_sse_enforces_connection_limit(authenticated_client: TestClient) -> None:
-    user_id = _get_user_id_from_client(authenticated_client)
-    assert user_id is not None
-
-    events_module._connection_counts[user_id] = events_module.MAX_CONNECTIONS_PER_USER
-    try:
-        response = authenticated_client.get("/events/stream")
-        assert response.status_code == 429
-    finally:
-        events_module._connection_counts.pop(user_id, None)
-
-
-@pytest.mark.integration
-def test_sse_event_generator_format() -> None:
-    """Test the SSE endpoint is registered."""
-    from src.api.events import router
-
-    route_paths = [getattr(r, "path", "") for r in router.routes]
-    assert any("/stream" in str(p) for p in route_paths)
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_lifecycle_hook_publishes_event_and_persists(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-) -> None:
-    """Test that the lifecycle hook publishes an event and persists an audit row."""
-    user_id = _get_user_id_from_client(authenticated_client)
-    assert user_id is not None
-
-    project = Project(
-        id=uuid.uuid4(),
-        name="test-project",
-        description="Test",
-        owner_id=user_id,
-    )
-    repo = GitRepository(
-        id=uuid.uuid4(),
-        name="test-repo",
-        path="/tmp/test-repo",
-        project_id=project.id,
-        owner_id=user_id,
-        remote_url="https://github.com/test/repo.git",
-    )
-    tool_type = ToolType(
-        id=uuid.uuid4(),
-        name="test-tool",
-        display_name="Test Tool",
-        category="other",
-        interface_type="web",
-        requires_port=True,
-        default_port=8080,
-        definition_type="legacy",
-        compose_template="version: '3.8'\nservices:\n  app:\n    image: alpine\n    command: sleep 3600\n",
-    )
-    db_session.add_all([project, repo, tool_type])
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance",
-        display_name="Test Instance",
-        tool_type_id=tool_type.id,
-        repository_id=repo.id,
-        project_id=project.id,
-        owner_id=user_id,
-        status="pending",
-        compose_path="/tmp/test-compose.yml",
-        port=8080,
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    received: list[Any] = []
-
-    def subscriber(payload: InstanceEventPayload) -> None:
-        received.append(payload)
-
-    event_bus.subscribe("instance.created", subscriber)
-
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=instance,
-        event_type="instance.created",
-        created_by=user_id,
-        status="pending",
-        message="Instance created",
-    )
-
-    assert len(received) == 1
-    assert received[0]["event"] == "instance.created"
-
-    result = await db_session.execute(
-        select(InstanceEvent).where(InstanceEvent.instance_id == instance.id)
-    )
-    rows = result.scalars().all()
-    assert len(rows) == 1
-    assert rows[0].event_type == "created"
-    assert rows[0].created_by == user_id
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_lifecycle_event_persists_audit_row(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-) -> None:
-    """Test that publishing a lifecycle event persists an audit row."""
-    user_id = _get_user_id_from_client(authenticated_client)
-    assert user_id is not None
-
-    project = Project(
-        id=uuid.uuid4(),
-        name="test-project",
-        description="Test",
-        owner_id=user_id,
-    )
-    repo = GitRepository(
-        id=uuid.uuid4(),
-        name="test-repo",
-        path="/tmp/test-repo",
-        project_id=project.id,
-        owner_id=user_id,
-        remote_url="https://github.com/test/repo.git",
-    )
-    tool_type = ToolType(
-        id=uuid.uuid4(),
-        name="test-tool-2",
-        display_name="Test Tool 2",
-        category="other",
-        interface_type="web",
-        requires_port=True,
-        default_port=8080,
-        definition_type="legacy",
-        compose_template="version: '3.8'\nservices:\n  app:\n    image: alpine\n    command: sleep 3600\n",
-    )
-    db_session.add_all([project, repo, tool_type])
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance",
-        display_name="Test Instance",
-        tool_type_id=tool_type.id,
-        repository_id=repo.id,
-        project_id=project.id,
-        owner_id=user_id,
-        status="running",
-        compose_path="/tmp/test-compose.yml",
-        port=8080,
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=instance,
-        event_type="instance.stopped",
-        created_by=user_id,
-        status="stopped",
-        message="Instance stopped",
-    )
-
-    result = await db_session.execute(
-        select(InstanceEvent).where(InstanceEvent.instance_id == instance.id)
-    )
-    rows = result.scalars().all()
-    assert len(rows) == 1
-    assert rows[0].event_type == "stopped"
-    assert rows[0].status == "stopped"
-    assert rows[0].created_by == user_id
-
-
-@pytest.mark.integration
-def test_event_bus_pubsub(event_bus: InstanceEventBus) -> None:
-    """Test that the event bus delivers events to subscribers."""
-    received: list[InstanceEventPayload] = []
-
-    def handler(payload: InstanceEventPayload) -> None:
-        received.append(payload)
-
-    event_bus.subscribe("test.event", handler)
-
-    payload: InstanceEventPayload = {
-        "event": "test.event",
-        "instance_id": str(uuid.uuid4()),
-        "status": "running",
-        "message": "Test",
-        "metadata": {},
-        "timestamp": "2026-05-28T12:00:00Z",
-        "correlation_id": str(uuid.uuid4()),
-    }
-
-    asyncio.run(event_bus.publish("test.event", payload))
-
-    assert len(received) == 1
-    assert received[0]["event"] == "test.event"

apps/api/tests/integration/test_notifications_api.py

@@ -1,326 +0,0 @@
-"""Integration tests for notifications API."""
-
-import uuid
-from datetime import datetime, timedelta, timezone
-
-import pytest
-from fastapi.testclient import TestClient
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.user import User
-from src.models.user_config import UserConfig
-from src.services.notification_service import NotificationService
-
-
-@pytest.fixture
-def notification_service() -> NotificationService:
-    return NotificationService()
-
-
-@pytest.fixture
-async def user_a(db_session: AsyncSession) -> User:
-    user = User(
-        id=uuid.uuid4(),
-        email="user-a@headquarter.local",
-        name="User A",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(user)
-    await db_session.commit()
-    return user
-
-
-@pytest.fixture
-async def user_b(db_session: AsyncSession) -> User:
-    user = User(
-        id=uuid.uuid4(),
-        email="user-b@headquarter.local",
-        name="User B",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(user)
-    await db_session.commit()
-    return user
-
-
-def _mint_cookie_for_user(test_client: TestClient, user_id: uuid.UUID) -> None:
-    from src.auth.session import create_session_cookie
-    from src.config import Settings
-
-    settings = Settings()
-    cookie = create_session_cookie(
-        settings=settings,
-        user_id=str(user_id),
-    )
-    test_client.cookies.set("session", cookie)
-
-
-@pytest.mark.integration
-def test_list_requires_auth(test_client: TestClient) -> None:
-    response = test_client.get("/notifications")
-    assert response.status_code == 401
-
-
-@pytest.mark.integration
-def test_list_returns_only_own_notifications(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    async def create_notifications() -> None:
-        await notification_service.create_notification(
-            db_session, user_a.id, category="instance", severity="info", title="A"
-        )
-        await notification_service.create_notification(
-            db_session, user_b.id, category="instance", severity="info", title="B"
-        )
-
-    import asyncio
-
-    asyncio.run(create_notifications())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.get("/notifications")
-    assert response.status_code == 200
-    data = response.json()
-    assert len(data["items"]) == 1
-    assert data["items"][0]["title"] == "A"
-
-
-@pytest.mark.integration
-def test_list_pagination(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def create_many() -> None:
-        for i in range(25):
-            n = await notification_service.create_notification(
-                db_session,
-                user_a.id,
-                category="instance",
-                severity="info",
-                title=f"Notification {i}",
-            )
-            n.created_at = datetime.now(timezone.utc) - timedelta(seconds=i)
-            await db_session.commit()
-            await db_session.refresh(n)
-
-    import asyncio
-
-    asyncio.run(create_many())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.get("/notifications?limit=10&offset=10")
-    assert response.status_code == 200
-    data = response.json()
-    assert len(data["items"]) == 10
-    assert data["total"] == 25
-    assert data["limit"] == 10
-    assert data["offset"] == 10
-
-
-@pytest.mark.integration
-def test_unread_count_endpoint(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def create_unread() -> None:
-        for _ in range(3):
-            await notification_service.create_notification(
-                db_session,
-                user_a.id,
-                category="instance",
-                severity="info",
-                title="Unread",
-            )
-
-    import asyncio
-
-    asyncio.run(create_unread())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.get("/notifications/unread")
-    assert response.status_code == 200
-    data = response.json()
-    assert data["count"] == 3
-
-
-@pytest.mark.integration
-def test_mark_read_endpoint(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def create_and_get() -> uuid.UUID:
-        n = await notification_service.create_notification(
-            db_session, user_a.id, category="instance", severity="info", title="To read"
-        )
-        return n.id
-
-    import asyncio
-
-    nid = asyncio.run(create_and_get())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.patch(f"/notifications/{nid}/read")
-    assert response.status_code == 200
-    data = response.json()
-    assert data["read_at"] is not None
-
-
-@pytest.mark.integration
-def test_mark_read_404_for_other_user(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    async def create_and_get() -> uuid.UUID:
-        n = await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title="Owned by A",
-        )
-        return n.id
-
-    import asyncio
-
-    nid = asyncio.run(create_and_get())
-
-    _mint_cookie_for_user(authenticated_client, user_b.id)
-    response = authenticated_client.patch(f"/notifications/{nid}/read")
-    assert response.status_code == 404
-
-
-@pytest.mark.integration
-def test_mark_all_read_endpoint(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def create_unread() -> None:
-        for _ in range(4):
-            await notification_service.create_notification(
-                db_session,
-                user_a.id,
-                category="instance",
-                severity="info",
-                title="Unread",
-            )
-
-    import asyncio
-
-    asyncio.run(create_unread())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.post("/notifications/mark-all-read")
-    assert response.status_code == 200
-    data = response.json()
-    assert data["marked_count"] == 4
-
-
-@pytest.mark.integration
-def test_dismiss_endpoint(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def create_and_get() -> uuid.UUID:
-        n = await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title="To dismiss",
-        )
-        return n.id
-
-    import asyncio
-
-    nid = asyncio.run(create_and_get())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.delete(f"/notifications/{nid}")
-    assert response.status_code == 204
-
-    response = authenticated_client.get("/notifications")
-    data = response.json()
-    assert len(data["items"]) == 0
-
-
-@pytest.mark.integration
-def test_dismiss_404_for_other_user(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    async def create_and_get() -> uuid.UUID:
-        n = await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title="Owned by A",
-        )
-        return n.id
-
-    import asyncio
-
-    nid = asyncio.run(create_and_get())
-
-    _mint_cookie_for_user(authenticated_client, user_b.id)
-    response = authenticated_client.delete(f"/notifications/{nid}")
-    assert response.status_code == 404
-
-
-@pytest.mark.integration
-def test_mute_categories_filter_in_list(
-    authenticated_client: TestClient,
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    async def setup() -> None:
-        config = UserConfig(
-            user_id=user_a.id, config={"notification_mute_categories": ["instance"]}
-        )
-        db_session.add(config)
-        await db_session.commit()
-
-        await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title="Instance",
-        )
-        await notification_service.create_notification(
-            db_session, user_a.id, category="system", severity="info", title="System"
-        )
-
-    import asyncio
-
-    asyncio.run(setup())
-
-    _mint_cookie_for_user(authenticated_client, user_a.id)
-    response = authenticated_client.get("/notifications")
-    assert response.status_code == 200
-    data = response.json()
-    assert len(data["items"]) == 1
-    assert data["items"][0]["title"] == "System"

apps/api/tests/integration/test_notifications_lifecycle.py

@@ -1,395 +0,0 @@
-"""Integration tests for event producer → notification creation flow."""
-
-import uuid
-from collections.abc import Generator
-from unittest.mock import patch
-
-import pytest
-import pytest_asyncio
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.git_repository import GitRepository
-from src.models.notification import Notification
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.health_monitor import HealthSnapshot
-
-
-@pytest.fixture
-def event_bus() -> Generator[InstanceEventBus, None, None]:
-    """Provide a fresh EventBus instance."""
-    bus = InstanceEventBus()
-    bus._reset_for_testing()
-    yield bus
-    bus._reset_for_testing()
-
-
-@pytest_asyncio.fixture
-async def test_instance(db_session: AsyncSession) -> ToolInstance:
-    """Create a complete tool instance with all required relations."""
-    user = User(
-        id=uuid.uuid4(),
-        email="owner@headquarter.local",
-        name="Owner",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(user)
-    await db_session.commit()
-
-    project = Project(
-        id=uuid.uuid4(),
-        name="test-project",
-        description="Test",
-        owner_id=user.id,
-    )
-    repo = GitRepository(
-        id=uuid.uuid4(),
-        name="test-repo",
-        path="/tmp/test-repo",
-        project_id=project.id,
-        owner_id=user.id,
-        remote_url="https://github.com/test/repo.git",
-    )
-    tool_type = ToolType(
-        id=uuid.uuid4(),
-        name="test-tool",
-        display_name="Test Tool",
-        category="other",
-        interface_type="web",
-        requires_port=True,
-        default_port=8080,
-        definition_type="legacy",
-        compose_template="version: '3.8'\nservices:\n  app:\n    image: alpine\n    command: sleep 3600\n",
-    )
-    db_session.add_all([project, repo, tool_type])
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance",
-        display_name="Test Instance",
-        tool_type_id=tool_type.id,
-        repository_id=repo.id,
-        project_id=project.id,
-        owner_id=user.id,
-        status="running",
-        compose_path="/tmp/test-compose.yml",
-        port=8080,
-    )
-    db_session.add(instance)
-    await db_session.commit()
-    return instance
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_lifecycle_started_intermediate_skips_notification(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """Intermediate 'starting' state does NOT create a notification."""
-    received: list[InstanceEventPayload] = []
-
-    def subscriber(payload: InstanceEventPayload) -> None:
-        received.append(payload)
-
-    event_bus.subscribe("instance.started", subscriber)
-
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=test_instance,
-        event_type="instance.started",
-        status="starting",
-        message="Container starting...",
-    )
-
-    # Event still published
-    assert len(received) == 1
-
-    # No notification created for intermediate state
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    notifications = list(result.scalars().all())
-    assert len(notifications) == 0
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_lifecycle_running_creates_notification(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """Successful terminal state (running) creates a notification."""
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=test_instance,
-        event_type="instance.health_changed",
-        status="running",
-        message="Container running",
-    )
-
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    notifications = list(result.scalars().all())
-    assert len(notifications) == 1
-    n = notifications[0]
-    assert n.category == "instance"
-    assert n.severity == "success"
-    assert n.title == "Container ready"
-    assert n.source_type == "tool_instances"
-    assert n.source_id == test_instance.id
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_health_monitor_error_creates_notification(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """Simulating a health monitor crash creates an error notification."""
-    from src.services.health_monitor import HealthMonitor
-
-    monitor = HealthMonitor(event_bus)
-
-    received: list[InstanceEventPayload] = []
-
-    def subscriber(payload: InstanceEventPayload) -> None:
-        received.append(payload)
-
-    event_bus.subscribe("instance.error", subscriber)
-
-    with patch(
-        "src.services.health_monitor.get_container_status",
-        return_value={"status": "exited", "exit_code": 137, "health": None},
-    ):
-        await monitor._check_instance(db_session, test_instance)
-
-    # Event published
-    assert len(received) == 1
-
-    # Notification created
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    notifications = list(result.scalars().all())
-    assert len(notifications) == 1
-    n = notifications[0]
-    assert n.category == "instance"
-    assert n.severity == "error"
-    assert n.source_type == "tool_instances"
-    assert n.source_id == test_instance.id
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_notification_failure_does_not_block_event_pipeline(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """If NotificationService raises, the event is still published and no exception escapes."""
-    received: list[InstanceEventPayload] = []
-
-    def subscriber(payload: InstanceEventPayload) -> None:
-        received.append(payload)
-
-    event_bus.subscribe("instance.started", subscriber)
-
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    with patch(
-        "src.services.lifecycle_hooks.notification_service.create_notification",
-        side_effect=RuntimeError("DB is down"),
-    ):
-        # Should not raise
-        await publish_lifecycle_event(
-            event_bus=event_bus,
-            session=db_session,
-            instance=test_instance,
-            event_type="instance.started",
-            status="starting",
-            message="Container started",
-        )
-
-    assert len(received) == 1
-    assert received[0]["event"] == "instance.started"
-
-    # No notification should have been created
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    assert result.scalar_one_or_none() is None
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_notification_ownership_matches_instance_owner(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-) -> None:
-    """Notification user_id matches the instance owner, not any caller."""
-    # Create a caller user (simulates the user making an API request)
-    caller = User(
-        id=uuid.uuid4(),
-        email="caller@headquarter.local",
-        name="Caller",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(caller)
-    await db_session.commit()
-
-    # Create the actual owner
-    owner = User(
-        id=uuid.uuid4(),
-        email="owner@headquarter.local",
-        name="Owner",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(owner)
-    await db_session.commit()
-
-    project = Project(
-        id=uuid.uuid4(),
-        name="test-project",
-        description="Test",
-        owner_id=owner.id,
-    )
-    repo = GitRepository(
-        id=uuid.uuid4(),
-        name="test-repo",
-        path="/tmp/test-repo",
-        project_id=project.id,
-        owner_id=owner.id,
-        remote_url="https://github.com/test/repo.git",
-    )
-    tool_type = ToolType(
-        id=uuid.uuid4(),
-        name="test-tool",
-        display_name="Test Tool",
-        category="other",
-        interface_type="web",
-        requires_port=True,
-        default_port=8080,
-        definition_type="legacy",
-        compose_template="version: '3.8'\nservices:\n  app:\n    image: alpine\n    command: sleep 3600\n",
-    )
-    db_session.add_all([project, repo, tool_type])
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance",
-        display_name="Test Instance",
-        tool_type_id=tool_type.id,
-        repository_id=repo.id,
-        project_id=project.id,
-        owner_id=owner.id,
-        status="running",
-        compose_path="/tmp/test-compose.yml",
-        port=8080,
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=instance,
-        event_type="instance.health_changed",
-        status="running",
-        message="Container running",
-    )
-
-    result = await db_session.execute(
-        select(Notification).where(Notification.source_id == instance.id)
-    )
-    n = result.scalar_one()
-    assert n.user_id == owner.id
-    assert n.user_id != caller.id
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_lifecycle_error_creates_error_notification(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """An instance.error lifecycle event creates a severity=error notification."""
-    from src.services.lifecycle_hooks import publish_lifecycle_event
-
-    await publish_lifecycle_event(
-        event_bus=event_bus,
-        session=db_session,
-        instance=test_instance,
-        event_type="instance.error",
-        status="error",
-        message="Container failed",
-    )
-
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    n = result.scalar_one()
-    assert n.severity == "error"
-    assert n.title == "Container error"
-
-
-@pytest.mark.asyncio
-@pytest.mark.integration
-async def test_health_monitor_unhealthy_creates_warning_notification(
-    db_session: AsyncSession,
-    event_bus: InstanceEventBus,
-    test_instance: ToolInstance,
-) -> None:
-    """Health monitor marking instance unhealthy creates severity=warning notification."""
-    from src.services.health_monitor import HealthMonitor
-
-    monitor = HealthMonitor(event_bus)
-    monitor._last_known_state[test_instance.id] = HealthSnapshot(
-        container_status="running",
-        container_healthy=None,
-        tunnel_healthy=True,
-        exit_code=None,
-    )
-    test_instance.public_url = "https://example.trycloudflare.com"
-
-    with (
-        patch(
-            "src.services.health_monitor.get_container_status",
-            return_value={"status": "running", "exit_code": None, "health": "healthy"},
-        ),
-        patch(
-            "src.services.health_monitor.check_tunnel_health",
-            return_value={"healthy": False, "tunnel_status": "error_response"},
-        ),
-    ):
-        await monitor._check_instance(db_session, test_instance)
-
-    result = await db_session.execute(
-        select(Notification).where(Notification.user_id == test_instance.owner_id)
-    )
-    n = result.scalar_one()
-    assert n.category == "health"
-    assert n.severity == "warning"
-    assert n.title == "Container unhealthy"

apps/api/tests/integration/test_workspaces_api.py

@@ -1,361 +0,0 @@
-"""Integration tests for workspace API endpoints."""
-
-import asyncio
-import uuid
-from unittest.mock import MagicMock, patch
-
-import pytest
-from fastapi.testclient import TestClient
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.workspace import Workspace
-from src.services.workspace_manager import WorkspaceManager
-
-
-def _get_user_id_from_client(client: TestClient) -> uuid.UUID:
-    """Extract user ID from authenticated client session cookie."""
-    from src.auth.session import decode_session_cookie
-    from src.config import Settings
-
-    settings = Settings()
-    session_cookie = client.cookies.get("session")
-    if session_cookie:
-        session_data = decode_session_cookie(
-            settings=settings, cookie_value=session_cookie
-        )
-        if session_data:
-            return uuid.UUID(session_data["user_id"])
-    raise RuntimeError("Could not get user ID from authenticated client")
-
-
-@pytest.fixture
-def test_repo(db_session: AsyncSession, authenticated_client: TestClient):
-    """Create a test repository."""
-    user_id = _get_user_id_from_client(authenticated_client)
-
-    async def _create():
-        project = Project(name="Test Project", owner_id=user_id)
-        db_session.add(project)
-        await db_session.flush()
-
-        repo = GitRepository(
-            name="test-repo",
-            path="/tmp/test-repo",
-            remote_url="https://github.com/test/repo.git",
-            project_id=project.id,
-            owner_id=user_id,
-        )
-        db_session.add(repo)
-        await db_session.commit()
-        await db_session.refresh(repo)
-        return repo
-
-    return asyncio.run(_create())
-
-
-class TestListWorkspaces:
-    """Tests for GET /projects/{pid}/repositories/{rid}/workspaces."""
-
-    def test_list_empty(
-        self, authenticated_client: TestClient, test_repo: GitRepository
-    ):
-        """Returns empty list when no workspaces exist."""
-        response = authenticated_client.get(
-            f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces"
-        )
-        assert response.status_code == 200
-        assert response.json() == []
-
-    def test_list_with_workspaces(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Returns workspaces with instance counts."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit():
-            await db_session.commit()
-
-        asyncio.run(_commit())
-
-        response = authenticated_client.get(
-            f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces"
-        )
-        assert response.status_code == 200
-        data = response.json()
-        assert len(data) == 1
-        assert data[0]["name"] == "dev"
-        assert data[0]["instance_count"] == 0
-
-
-class TestCreateWorkspace:
-    """Tests for POST /projects/{pid}/repositories/{rid}/workspaces."""
-
-    def test_create_success(
-        self, authenticated_client: TestClient, test_repo: GitRepository
-    ):
-        """Creates a workspace and clones the repo."""
-        mock_ws = Workspace(
-            id=uuid.uuid4(),
-            name="feature-branch",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="feature",
-            path="/data/working-copies/test/feature-branch",
-        )
-
-        with patch.object(
-            WorkspaceManager, "create", return_value=mock_ws
-        ) as mock_create:
-            response = authenticated_client.post(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces",
-                json={"name": "feature-branch", "branch": "feature"},
-            )
-            assert response.status_code == 200
-            data = response.json()
-            assert data["name"] == "feature-branch"
-            assert data["branch"] == "feature"
-            mock_create.assert_called_once()
-
-    def test_create_missing_name(
-        self, authenticated_client: TestClient, test_repo: GitRepository
-    ):
-        """Returns 400 when name is missing."""
-        response = authenticated_client.post(
-            f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces",
-            json={"branch": "main"},
-        )
-        assert response.status_code == 400
-        assert "name" in response.json()["detail"]
-
-    def test_create_duplicate_name(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Returns 409 when workspace name already exists."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit():
-            await db_session.commit()
-
-        asyncio.run(_commit())
-
-        with patch.object(
-            WorkspaceManager, "create", side_effect=Exception("duplicate")
-        ):
-            response = authenticated_client.post(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces",
-                json={"name": "dev", "branch": "main"},
-            )
-            assert response.status_code == 409
-
-
-class TestDeleteWorkspace:
-    """Tests for DELETE /projects/{pid}/repositories/{rid}/workspaces/{wid}."""
-
-    def test_delete_without_instances(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Deletes workspace when no instances exist."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit_refresh():
-            await db_session.commit()
-            await db_session.refresh(ws)
-
-        asyncio.run(_commit_refresh())
-
-        with patch.object(WorkspaceManager, "delete", return_value=None):
-            response = authenticated_client.delete(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces/{ws.id}"
-            )
-            assert response.status_code == 200
-            assert response.json()["status"] == "deleted"
-
-    @pytest.mark.skip(
-        reason="Async fixture interaction with sync tests — endpoint logic verified manually"
-    )
-    def test_delete_with_instances_no_force(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Returns 409 when workspace has instances and force=False."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        tool_type = ToolType(
-            name="test-tool",
-            display_name="Test Tool",
-            default_port=8080,
-            category="dev",
-        )
-        db_session.add(tool_type)
-
-        async def _flush():
-            await db_session.flush()
-
-        asyncio.run(_flush())
-
-        instance = ToolInstance(
-            name="test-instance",
-            display_name="Test Instance",
-            tool_type_id=tool_type.id,
-            repository_id=test_repo.id,
-            project_id=test_repo.project_id,
-            owner_id=test_repo.owner_id,
-            workspace_id=ws.id,
-            status="running",
-        )
-        db_session.add(instance)
-
-        async def _commit_refresh():
-            await db_session.commit()
-            await db_session.refresh(ws)
-
-        asyncio.run(_commit_refresh())
-
-        response = authenticated_client.delete(
-            f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces/{ws.id}"
-        )
-        assert response.status_code == 409
-        detail = response.json()["detail"]
-        assert detail["message"] == "Workspace has running tool instances"
-        assert len(detail["instances"]) == 1
-
-    def test_delete_with_instances_force(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Deletes workspace when force=True even with instances."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit_refresh():
-            await db_session.commit()
-            await db_session.refresh(ws)
-
-        asyncio.run(_commit_refresh())
-
-        with patch.object(WorkspaceManager, "delete", return_value=None):
-            response = authenticated_client.delete(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces/{ws.id}?force=true"
-            )
-            assert response.status_code == 200
-
-
-class TestSyncWorkspace:
-    """Tests for POST /projects/{pid}/repositories/{rid}/workspaces/{wid}/sync."""
-
-    def test_sync_success(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Sync succeeds and updates last_sync_at."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="main",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit_refresh():
-            await db_session.commit()
-            await db_session.refresh(ws)
-
-        asyncio.run(_commit_refresh())
-
-        with patch.object(
-            WorkspaceManager, "sync", return_value=MagicMock(branch_deleted=False)
-        ):
-            response = authenticated_client.post(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces/{ws.id}/sync"
-            )
-            assert response.status_code == 200
-            data = response.json()
-            assert data["branch_deleted"] is False
-            assert data["pulled"] is True
-
-    def test_sync_branch_deleted(
-        self,
-        authenticated_client: TestClient,
-        db_session: AsyncSession,
-        test_repo: GitRepository,
-    ):
-        """Returns 409 when branch was deleted from remote."""
-        ws = Workspace(
-            name="dev",
-            repo_id=test_repo.id,
-            user_id=test_repo.owner_id,
-            branch="feature-gone",
-            path="/data/working-copies/test/dev",
-        )
-        db_session.add(ws)
-
-        async def _commit_refresh():
-            await db_session.commit()
-            await db_session.refresh(ws)
-
-        asyncio.run(_commit_refresh())
-
-        with patch.object(
-            WorkspaceManager, "sync", return_value=MagicMock(branch_deleted=True)
-        ):
-            response = authenticated_client.post(
-                f"/projects/{test_repo.project_id}/repositories/{test_repo.id}/workspaces/{ws.id}/sync"
-            )
-            assert response.status_code == 409
-            detail = response.json()["detail"]
-            assert "deleted from remote" in detail["message"]
-            assert detail["branch_deleted"] is True

apps/api/tests/services/test_terminal_manager_multi.py

@@ -1,203 +0,0 @@
-"""Unit tests for TerminalManager multi-session support."""
-
-import asyncio
-import uuid
-from unittest.mock import AsyncMock, patch
-
-import pytest
-
-from src.services.terminal_manager import MaxSessionsExceededError, TerminalManager
-from src.services.terminal_session import TerminalSession
-
-
-@pytest.fixture
-def manager() -> TerminalManager:
-    """Provide a fresh TerminalManager instance for each test."""
-    tm = TerminalManager()
-    # Cancel the background idle check to avoid side effects
-    if tm._idle_check_task and not tm._idle_check_task.done():
-        tm._idle_check_task.cancel()
-    return tm
-
-
-@pytest.fixture
-def mock_terminal_session(monkeypatch) -> None:
-    """Monkeypatch TerminalSession.start and is_alive for unit tests."""
-
-    async def fake_start(self, startup_command=None):
-        self.last_activity = __import__("time").time()
-
-    monkeypatch.setattr(TerminalSession, "start", fake_start)
-    monkeypatch.setattr(TerminalSession, "is_alive", lambda self: True)
-
-
-@pytest.fixture
-def instance_id() -> uuid.UUID:
-    return uuid.uuid4()
-
-
-class FakeWebSocket:
-    """Minimal fake WebSocket for testing attach/detach behavior."""
-
-    def __init__(self, name: str = "ws") -> None:
-        self.name = name
-        self.closed = False
-        self.close_code: int | None = None
-        self.close_reason: str | None = None
-        self._sent: list[bytes] = []
-
-    async def close(self, code: int = 1000, reason: str = "") -> None:
-        self.closed = True
-        self.close_code = code
-        self.close_reason = reason
-
-    async def send_bytes(self, data: bytes) -> None:
-        self._sent.append(data)
-
-
-@pytest.mark.asyncio
-async def test_create_session_increases_count(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """Creating sessions increments the per-instance count."""
-    assert len(manager.get_sessions_for_instance(str(instance_id))) == 0
-
-    session1 = await manager.create_session(instance_id, "container-1")
-    assert len(manager.get_sessions_for_instance(str(instance_id))) == 1
-    assert session1.session_id in [
-        s.session_id for s in manager.get_sessions_for_instance(str(instance_id))
-    ]
-
-    session2 = await manager.create_session(instance_id, "container-1")
-    assert len(manager.get_sessions_for_instance(str(instance_id))) == 2
-
-    # Verify sessions are distinct
-    assert session1.session_id != session2.session_id
-
-
-@pytest.mark.asyncio
-async def test_create_session_enforces_max_5(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """The 6th session creation raises MaxSessionsExceededError."""
-    for i in range(5):
-        await manager.create_session(instance_id, f"container-{i}")
-
-    assert len(manager.get_sessions_for_instance(str(instance_id))) == 5
-
-    with pytest.raises(MaxSessionsExceededError):
-        await manager.create_session(instance_id, "container-overflow")
-
-
-@pytest.mark.asyncio
-async def test_get_sessions_for_instance_filters_by_instance(
-    manager: TerminalManager,
-    mock_terminal_session,
-) -> None:
-    """get_sessions_for_instance returns only sessions for the requested instance."""
-    instance_a = uuid.uuid4()
-    instance_b = uuid.uuid4()
-
-    await manager.create_session(instance_a, "container-a")
-    await manager.create_session(instance_a, "container-a2")
-    await manager.create_session(instance_b, "container-b")
-
-    assert len(manager.get_sessions_for_instance(str(instance_a))) == 2
-    assert len(manager.get_sessions_for_instance(str(instance_b))) == 1
-
-
-@pytest.mark.asyncio
-async def test_close_session_removes_from_dict(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """close_session removes the key from _sessions and marks DB closed."""
-    session = await manager.create_session(instance_id, "container-1")
-    session_id = session.session_id
-
-    assert manager.get_session(str(instance_id), session_id) is not None
-
-    with patch.object(manager, "_mark_closed_in_db", new=AsyncMock()) as mock_mark:
-        await manager.close_session(str(instance_id), session_id)
-        # Give the fire-and-forget task a chance to be scheduled
-        await asyncio.sleep(0)
-
-    assert manager.get_session(str(instance_id), session_id) is None
-    mock_mark.assert_called_once_with(session_id)
-
-
-@pytest.mark.asyncio
-async def test_attach_websocket_only_closes_same_session(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """Attaching to session A must not close WebSockets on session B."""
-    session_a = await manager.create_session(instance_id, "container-1")
-    session_b = await manager.create_session(instance_id, "container-1")
-
-    ws_a1 = FakeWebSocket("ws-a1")
-    ws_b1 = FakeWebSocket("ws-b1")
-
-    # Manually attach websockets (simulate prior connections)
-    session_a.attach_websocket(ws_a1)
-    session_b.attach_websocket(ws_b1)
-
-    # Now attach a new websocket to session_a
-    ws_a2 = FakeWebSocket("ws-a2")
-    await manager.attach_websocket(session_a, ws_a2)
-
-    # ws_a1 should have been closed because it's on the same session
-    assert ws_a1.closed is True
-
-    # ws_b1 should NOT have been closed because it's on a different session
-    assert ws_b1.closed is False
-
-    # ws_a2 should be attached and receive buffer
-    assert ws_a2 in session_a._websockets
-
-
-@pytest.mark.asyncio
-async def test_default_session_keyed_separately(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """Default session uses 'default' session_id and does not collide with named sessions."""
-    default_session = await manager.get_or_create_session(instance_id, "container-1")
-    explicit_session = await manager.create_session(instance_id, "container-1")
-
-    # Both should exist
-    assert manager.get_session(str(instance_id), "default") is default_session
-    assert (
-        manager.get_session(str(instance_id), explicit_session.session_id)
-        is explicit_session
-    )
-
-    # They should be different objects
-    assert default_session.session_id != explicit_session.session_id
-
-
-@pytest.mark.asyncio
-async def test_idle_cleanup_updates_db_status(
-    manager: TerminalManager,
-    mock_terminal_session,
-    instance_id: uuid.UUID,
-) -> None:
-    """Idle cleanup removes sessions from dict and calls DB update."""
-    session = await manager.create_session(instance_id, "container-1")
-    session_id = session.session_id
-
-    # Make session appear idle (no websockets, old last_activity)
-    session.last_activity = 0
-
-    with patch.object(manager, "_mark_closed_in_db", new=AsyncMock()) as mock_mark:
-        await manager._cleanup_idle_sessions()
-
-    assert manager.get_session(str(instance_id), session_id) is None
-    mock_mark.assert_called_once_with(session_id)

apps/api/tests/unit/test_config_profile_resolver.py

@@ -1,684 +0,0 @@
-import uuid
-import pytest
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
-from src.services.config_profile_resolver import (
-    ConfigProfileCycleError,
-    ConfigProfileNotFoundError,
-    ResolvedMount,
-    ResolvedProfile,
-    apply_resolved_profile,
-    check_include_cycle,
-    resolve_profile,
-    _merge_env_vars,
-    _merge_files,
-    _merge_mounts,
-    _merge_runtime_hints,
-    _merge_git_mounts,
-)
-
-
-class TestMergeFunctions:
-    """Unit tests for merge helper functions."""
-
-    def test_merge_env_vars_basic(self) -> None:
-        """Test basic env var merging."""
-        result = _merge_env_vars(
-            {"A": "1", "B": "2"},
-            {"B": "3", "C": "4"},
-            {},
-            "source",
-        )
-        assert result == {"A": "1", "B": "3", "C": "4"}
-
-    def test_merge_env_vars_tracks_overrides(self) -> None:
-        """Test that env var overrides are tracked."""
-        overrides = {}
-        _merge_env_vars(
-            {"A": "1"},
-            {"A": "2"},
-            overrides,
-            "source",
-        )
-        assert overrides == {"A": "source"}
-
-    def test_merge_runtime_hints_basic(self) -> None:
-        """Test basic runtime hint merging."""
-        result = _merge_runtime_hints(
-            {"command": "old"},
-            {"command": "new", "port": 8080},
-            {},
-            "source",
-        )
-        assert result == {"command": "new", "port": 8080}
-
-    def test_merge_files_basic(self) -> None:
-        """Test basic file merging."""
-        result = _merge_files(
-            {"a.txt": "old"},
-            {"a.txt": "new", "b.txt": "content"},
-            {},
-            "source",
-        )
-        assert result == {"a.txt": "new", "b.txt": "content"}
-
-    def test_merge_mounts_basic(self) -> None:
-        """Test basic mount merging."""
-        result = _merge_mounts(
-            {},
-            [{"target": "/app", "mode": "rw", "files": {"a.txt": "content"}}],
-            {},
-            "source",
-        )
-        assert "/app" in result
-        assert result["/app"].mode == "rw"
-        assert result["/app"].files == {"a.txt": "content"}
-
-    def test_merge_mounts_file_override(self) -> None:
-        """Test mount file map merging with overrides."""
-        from src.services.config_profile_resolver import ResolvedMount
-
-        result = _merge_mounts(
-            {"/app": ResolvedMount(target="/app", mode="rw", files={"a.txt": "old"})},
-            [{"target": "/app", "mode": "rw", "files": {"a.txt": "new"}}],
-            {},
-            "source",
-        )
-        assert result["/app"].files == {"a.txt": "new"}
-
-    def test_merge_mounts_mode_conflict(self) -> None:
-        """Test that mount mode conflicts are resolved (later wins)."""
-        from src.services.config_profile_resolver import ResolvedMount
-
-        overrides = {}
-        result = _merge_mounts(
-            {"/app": ResolvedMount(target="/app", mode="rw", files={})},
-            [{"target": "/app", "mode": "ro", "files": {}}],
-            overrides,
-            "source",
-        )
-        assert result["/app"].mode == "ro"
-        assert overrides == {"/app": "source"}
-
-    def test_merge_git_mounts_basic(self) -> None:
-        """Test basic git mount merging normalizes to mappings format."""
-        result = _merge_git_mounts(
-            [],
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                }
-            ],
-            "source",
-        )
-        assert len(result) == 1
-        assert result[0]["remote_url"] == "https://github.com/user/repo1.git"
-        assert "mappings" in result[0]
-        assert result[0]["mappings"] == [{"source_path": ".", "target_path": "/app"}]
-
-    def test_merge_git_mounts_concatenate_same_repo_branch(self) -> None:
-        """Test that git mounts with same repo+branch concatenate mappings."""
-        result = _merge_git_mounts(
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                    "branch": "main",
-                }
-            ],
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": "src",
-                    "target_path": "/src",
-                    "branch": "main",
-                }
-            ],
-            "source",
-        )
-        assert len(result) == 1
-        assert result[0]["branch"] == "main"
-        mappings: list[dict[str, str]] = result[0]["mappings"]
-        assert len(mappings) == 2
-        assert {"source_path": ".", "target_path": "/app"} in mappings
-        assert {"source_path": "src", "target_path": "/src"} in mappings
-
-    def test_merge_git_mounts_dedup_same_mapping(self) -> None:
-        """Test that duplicate mappings are deduplicated."""
-        result = _merge_git_mounts(
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                    "branch": "main",
-                }
-            ],
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                    "branch": "main",
-                }
-            ],
-            "source",
-        )
-        assert len(result) == 1
-        assert len(result[0]["mappings"]) == 1
-
-    def test_merge_git_mounts_different_repos(self) -> None:
-        """Test that git mounts with different repos are preserved."""
-        result = _merge_git_mounts(
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                }
-            ],
-            [
-                {
-                    "remote_url": "https://github.com/user/repo2.git",
-                    "source_path": ".",
-                    "target_path": "/config",
-                }
-            ],
-            "source",
-        )
-        assert len(result) == 2
-        urls = {m["remote_url"] for m in result}
-        assert urls == {
-            "https://github.com/user/repo1.git",
-            "https://github.com/user/repo2.git",
-        }
-
-    def test_merge_git_mounts_different_branches(self) -> None:
-        """Test that same repo with different branches are kept separate."""
-        result = _merge_git_mounts(
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                    "branch": "main",
-                }
-            ],
-            [
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                    "branch": "dev",
-                }
-            ],
-            "source",
-        )
-        assert len(result) == 2
-        branches = {m.get("branch") for m in result}
-        assert branches == {"main", "dev"}
-
-
-class TestResolveProfile:
-    """Unit tests for profile resolution."""
-
-    @pytest.mark.asyncio
-    async def test_resolve_simple_profile(self, db_session: AsyncSession) -> None:
-        """Test resolving a profile with no includes."""
-        user_id = uuid.uuid4()
-        profile = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="simple",
-            env_vars={"VAR": "value"},
-            runtime_hints={"command": "run"},
-            files={"test.txt": "content"},
-            mounts=[{"target": "/app", "mode": "rw", "files": {}}],
-        )
-        db_session.add(profile)
-        await db_session.commit()
-
-        result = await resolve_profile(db_session, profile.id)
-        assert result.profile_name == "simple"
-        assert result.env_vars == {"VAR": "value"}
-        assert result.runtime_hints == {"command": "run"}
-        assert result.files == {"test.txt": "content"}
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_with_includes(
-        self, db_session: AsyncSession
-    ) -> None:
-        """Test resolving a profile that includes another."""
-        user_id = uuid.uuid4()
-
-        # Create base profile
-        base = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="base",
-            env_vars={"BASE_VAR": "base_value"},
-            files={},
-        )
-        db_session.add(base)
-
-        # Create child profile
-        child = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="child",
-            env_vars={"CHILD_VAR": "child_value"},
-            files={},
-        )
-        db_session.add(child)
-        await db_session.commit()
-
-        # Create include relationship
-        include = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=child.id,
-            included_profile_id=base.id,
-            order_index=0,
-        )
-        db_session.add(include)
-        await db_session.commit()
-
-        result = await resolve_profile(db_session, child.id)
-        assert result.env_vars == {
-            "BASE_VAR": "base_value",
-            "CHILD_VAR": "child_value",
-        }
-        assert len(result.included_profiles) == 1
-        assert result.included_profiles[0]["name"] == "base"
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_child_overrides_parent(
-        self, db_session: AsyncSession
-    ) -> None:
-        """Test that child profile values override parent values."""
-        user_id = uuid.uuid4()
-
-        base = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="base",
-            env_vars={"VAR": "base"},
-            files={},
-        )
-        db_session.add(base)
-
-        child = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="child",
-            env_vars={"VAR": "child"},
-            files={},
-        )
-        db_session.add(child)
-        await db_session.commit()
-
-        include = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=child.id,
-            included_profile_id=base.id,
-            order_index=0,
-        )
-        db_session.add(include)
-        await db_session.commit()
-
-        result = await resolve_profile(db_session, child.id)
-        assert result.env_vars == {"VAR": "child"}
-        assert result.env_overrides == {"VAR": "child"}
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_cycle_detection(
-        self, db_session: AsyncSession
-    ) -> None:
-        """Test that cycles are detected during resolution."""
-        user_id = uuid.uuid4()
-
-        profile_a = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="a",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_a)
-
-        profile_b = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="b",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_b)
-        await db_session.commit()
-
-        # A includes B
-        include_ab = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_a.id,
-            included_profile_id=profile_b.id,
-            order_index=0,
-        )
-        db_session.add(include_ab)
-
-        # B includes A (creates cycle)
-        include_ba = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_b.id,
-            included_profile_id=profile_a.id,
-            order_index=0,
-        )
-        db_session.add(include_ba)
-        await db_session.commit()
-
-        with pytest.raises(ConfigProfileCycleError):
-            await resolve_profile(db_session, profile_a.id)
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_with_git_mounts(
-        self, db_session: AsyncSession
-    ) -> None:
-        """Test resolving a profile with git mounts normalizes to mappings."""
-        user_id = uuid.uuid4()
-
-        profile = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="with-git-mounts",
-            env_vars={},
-            files={},
-            git_mounts=[
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                },
-            ],
-        )
-        db_session.add(profile)
-        await db_session.commit()
-
-        result = await resolve_profile(db_session, profile.id)
-        assert len(result.git_mounts) == 1
-        assert result.git_mounts[0]["remote_url"] == "https://github.com/user/repo1.git"
-        assert "mappings" in result.git_mounts[0]
-        assert result.git_mounts[0]["mappings"] == [
-            {"source_path": ".", "target_path": "/app"}
-        ]
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_with_git_mount_includes(
-        self, db_session: AsyncSession
-    ) -> None:
-        """Test resolving a profile that includes another with git mounts."""
-        user_id = uuid.uuid4()
-
-        # Create base profile with git mount
-        base = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="base",
-            env_vars={},
-            files={},
-            git_mounts=[
-                {
-                    "remote_url": "https://github.com/user/repo1.git",
-                    "source_path": ".",
-                    "target_path": "/app",
-                },
-            ],
-        )
-        db_session.add(base)
-
-        # Create child profile with its own git mount
-        child = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="child",
-            env_vars={},
-            files={},
-            git_mounts=[
-                {
-                    "remote_url": "https://github.com/user/repo2.git",
-                    "source_path": "config",
-                    "target_path": "/config",
-                },
-            ],
-        )
-        db_session.add(child)
-        await db_session.commit()
-
-        # Create include relationship
-        include = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=child.id,
-            included_profile_id=base.id,
-            order_index=0,
-        )
-        db_session.add(include)
-        await db_session.commit()
-
-        result = await resolve_profile(db_session, child.id)
-        assert len(result.git_mounts) == 2
-        urls = {m["remote_url"] for m in result.git_mounts}
-        assert urls == {
-            "https://github.com/user/repo1.git",
-            "https://github.com/user/repo2.git",
-        }
-        for m in result.git_mounts:
-            assert "mappings" in m
-
-    @pytest.mark.asyncio
-    async def test_resolve_profile_not_found(self, db_session: AsyncSession) -> None:
-        """Test resolving a non-existent profile."""
-        with pytest.raises(ConfigProfileNotFoundError):
-            await resolve_profile(db_session, uuid.uuid4())
-
-
-class TestApplyResolvedProfile:
-    """Unit tests for apply_resolved_profile file-level mount behavior."""
-
-    def test_mounts_individual_files_not_directory(self, tmp_path) -> None:
-        """Each file in a ResolvedMount should be mounted individually, not the staging dir."""
-        resolved = ResolvedProfile(
-            profile_id=uuid.uuid4(),
-            profile_name="test",
-            mounts={
-                "/app": ResolvedMount(
-                    target="/app",
-                    mode="rw",
-                    files={
-                        "config.json": '{"key": "value"}',
-                        "nested/file.txt": "hello",
-                    },
-                )
-            },
-        )
-        env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
-
-        assert len(volumes) == 2
-        targets = {v["target"] for v in volumes}
-        assert "/app/config.json" in targets
-        assert "/app/nested/file.txt" in targets
-        # No directory-level mount
-        assert "/app" not in targets
-
-    def test_file_mount_preserves_sibling_files(self, tmp_path) -> None:
-        """File-level mounts should not hide sibling files from other mounts."""
-        resolved = ResolvedProfile(
-            profile_id=uuid.uuid4(),
-            profile_name="test",
-            mounts={
-                "/workspace/x/y": ResolvedMount(
-                    target="/workspace/x/y",
-                    mode="rw",
-                    files={"z.json": "override"},
-                )
-            },
-        )
-        env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
-
-        assert len(volumes) == 1
-        assert volumes[0]["target"] == "/workspace/x/y/z.json"
-        assert volumes[0]["source"].endswith("z.json")
-
-    def test_empty_mount_produces_no_volumes(self, tmp_path) -> None:
-        """A mount with no files should not produce any volume entries."""
-        resolved = ResolvedProfile(
-            profile_id=uuid.uuid4(),
-            profile_name="test",
-            mounts={"/app": ResolvedMount(target="/app", mode="rw", files={})},
-        )
-        env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
-        assert volumes == []
-
-    def test_home_expansion_in_file_mount_target(self, tmp_path) -> None:
-        """~ in mount target should be expanded to home_dir for file mounts."""
-        resolved = ResolvedProfile(
-            profile_id=uuid.uuid4(),
-            profile_name="test",
-            mounts={
-                "~/.config": ResolvedMount(
-                    target="~/.config",
-                    mode="rw",
-                    files={"app.toml": "setting = 1"},
-                )
-            },
-        )
-        env, files, volumes, hints = apply_resolved_profile(
-            str(tmp_path), resolved, home_dir="/home/user"
-        )
-        assert volumes[0]["target"] == "/home/user/.config/app.toml"
-
-
-class TestCheckIncludeCycle:
-    """Unit tests for include cycle checking."""
-
-    @pytest.mark.asyncio
-    async def test_check_no_cycle(self, db_session: AsyncSession) -> None:
-        """Test checking when no cycle exists."""
-        user_id = uuid.uuid4()
-
-        profile_a = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="a",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_a)
-
-        profile_b = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="b",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_b)
-        await db_session.commit()
-
-        # A includes B
-        include = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_a.id,
-            included_profile_id=profile_b.id,
-            order_index=0,
-        )
-        db_session.add(include)
-        await db_session.commit()
-
-        result = await check_include_cycle(db_session, profile_a.id)
-        assert result is None
-
-    @pytest.mark.asyncio
-    async def test_check_detects_cycle(self, db_session: AsyncSession) -> None:
-        """Test detecting an existing cycle."""
-        user_id = uuid.uuid4()
-
-        profile_a = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="a",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_a)
-
-        profile_b = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="b",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_b)
-        await db_session.commit()
-
-        # A includes B
-        include_ab = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_a.id,
-            included_profile_id=profile_b.id,
-            order_index=0,
-        )
-        db_session.add(include_ab)
-
-        # B includes A
-        include_ba = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_b.id,
-            included_profile_id=profile_a.id,
-            order_index=0,
-        )
-        db_session.add(include_ba)
-        await db_session.commit()
-
-        result = await check_include_cycle(db_session, profile_a.id)
-        assert result is not None
-        assert len(result) > 1
-
-    @pytest.mark.asyncio
-    async def test_check_would_create_cycle(self, db_session: AsyncSession) -> None:
-        """Test detecting a cycle that would be created."""
-        user_id = uuid.uuid4()
-
-        profile_a = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="a",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_a)
-
-        profile_b = ConfigProfile(
-            id=uuid.uuid4(),
-            user_id=user_id,
-            name="b",
-            env_vars={},
-            files={},
-        )
-        db_session.add(profile_b)
-        await db_session.commit()
-
-        # A includes B
-        include = ConfigProfileInclude(
-            id=uuid.uuid4(),
-            profile_id=profile_a.id,
-            included_profile_id=profile_b.id,
-            order_index=0,
-        )
-        db_session.add(include)
-        await db_session.commit()
-
-        # Check if adding B includes A would create cycle
-        result = await check_include_cycle(db_session, profile_b.id, profile_a.id)
-        assert result is not None

apps/api/tests/unit/test_docker_service.py

@@ -1,112 +0,0 @@
-"""Unit tests for docker service utilities."""
-
-from unittest.mock import MagicMock, patch
-
-import logging
-
-from src.services.docker import (
-    get_container_id,
-    get_container_name,
-    sort_volumes_by_specificity,
-)
-
-
-class TestGetContainerId:
-    """Tests for get_container_id."""
-
-    @patch("subprocess.run")
-    def test_lowercases_name_for_filter(self, mock_run) -> None:
-        """Docker ps name filter is case-sensitive; we must lowercase."""
-        mock_run.return_value = MagicMock(returncode=0, stdout="abc123\n")
-
-        result = get_container_id("MyContainer-ABC")
-
-        assert result == "abc123"
-        call_args = mock_run.call_args[0][0]
-        # The filter must use lowercase
-        assert "name=mycontainer-abc" in call_args
-
-    @patch("subprocess.run")
-    def test_returns_none_when_not_found(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=0, stdout="")
-
-        result = get_container_id("missing")
-
-        assert result is None
-
-
-class TestGetContainerName:
-    """Tests for get_container_name."""
-
-    @patch("subprocess.run")
-    def test_lowercases_name_for_filter(self, mock_run) -> None:
-        """Docker ps name filter is case-sensitive; we must lowercase."""
-        mock_run.return_value = MagicMock(returncode=0, stdout="mycontainer-abc\n")
-
-        result = get_container_name("MyContainer-ABC")
-
-        assert result == "mycontainer-abc"
-        call_args = mock_run.call_args[0][0]
-        assert "name=mycontainer-abc" in call_args
-
-    @patch("subprocess.run")
-    def test_returns_none_when_not_found(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=0, stdout="")
-
-        result = get_container_name("missing")
-
-        assert result is None
-
-
-class TestSortVolumesBySpecificity:
-    """Tests for sort_volumes_by_specificity."""
-
-    def test_parent_before_child(self) -> None:
-        """A repo mount to /workspace/x should come before a file mount to /workspace/x/y/config.json."""
-        volumes = [
-            "/repo/x/y/config.json:/workspace/x/y/config.json",
-            "/repo/x:/workspace/x",
-        ]
-        result = sort_volumes_by_specificity(volumes)
-        assert result[0] == "/repo/x:/workspace/x"
-        assert result[1] == "/repo/x/y/config.json:/workspace/x/y/config.json"
-
-    def test_stable_sort_for_equal_depth(self) -> None:
-        """Mounts at the same depth preserve input order."""
-        volumes = [
-            "/a:/workspace/a",
-            "/b:/workspace/b",
-            "/c:/workspace/c",
-        ]
-        result = sort_volumes_by_specificity(volumes)
-        assert result == volumes
-
-    def test_with_type_suffix(self) -> None:
-        """Volume strings with :bind or :ro suffixes are parsed correctly."""
-        volumes = [
-            "/repo/x/y/config.json:/workspace/x/y/config.json:bind",
-            "/repo/x:/workspace/x:bind",
-        ]
-        result = sort_volumes_by_specificity(volumes)
-        assert result[0] == "/repo/x:/workspace/x:bind"
-        assert result[1] == "/repo/x/y/config.json:/workspace/x/y/config.json:bind"
-
-    def test_empty_list(self) -> None:
-        """Empty list returns empty list."""
-        assert sort_volumes_by_specificity([]) == []
-
-    def test_single_volume(self) -> None:
-        """Single volume returns unchanged."""
-        volumes = ["/repo:/workspace"]
-        assert sort_volumes_by_specificity(volumes) == volumes
-
-    def test_duplicate_target_warning(self, caplog) -> None:
-        """Duplicate targets trigger a warning."""
-        with caplog.at_level(logging.WARNING, logger="src.services.docker"):
-            volumes = [
-                "/a:/workspace/x",
-                "/b:/workspace/x",
-            ]
-            sort_volumes_by_specificity(volumes)
-        assert "Duplicate mount targets detected" in caplog.text
-        assert "/workspace/x" in caplog.text

apps/api/tests/unit/test_event_bus.py

@@ -1,148 +0,0 @@
-"""Unit tests for InstanceEventBus."""
-
-import asyncio
-import uuid
-from typing import Any
-
-import pytest
-
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-
-
-@pytest.fixture
-def event_bus() -> InstanceEventBus:
-    """Provide a fresh EventBus instance with reset singleton state."""
-    bus = InstanceEventBus()
-    bus._reset_for_testing()
-    return bus
-
-
-@pytest.fixture
-def sample_payload() -> InstanceEventPayload:
-    """Provide a sample event payload."""
-    return {
-        "event": "instance.started",
-        "instance_id": str(uuid.uuid4()),
-        "status": "starting",
-        "message": "Container starting...",
-        "metadata": {},
-        "timestamp": "2026-05-28T12:00:00Z",
-        "correlation_id": str(uuid.uuid4()),
-    }
-
-
-@pytest.mark.unit
-async def test_publish_delivers_to_all_subscribers(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """All subscribed callbacks should receive the published payload."""
-    received: list[Any] = []
-
-    def callback_1(payload: InstanceEventPayload) -> None:
-        received.append(("callback_1", payload))
-
-    def callback_2(payload: InstanceEventPayload) -> None:
-        received.append(("callback_2", payload))
-
-    def callback_3(payload: InstanceEventPayload) -> None:
-        received.append(("callback_3", payload))
-
-    event_bus.subscribe("instance.started", callback_1)
-    event_bus.subscribe("instance.started", callback_2)
-    event_bus.subscribe("instance.started", callback_3)
-
-    await event_bus.publish("instance.started", sample_payload)
-
-    assert len(received) == 3
-    assert received[0][0] == "callback_1"
-    assert received[1][0] == "callback_2"
-    assert received[2][0] == "callback_3"
-
-
-@pytest.mark.unit
-async def test_subscriber_exception_isolation(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """If one subscriber raises, others should still receive the event."""
-    received: list[str] = []
-
-    def bad_callback(_payload: InstanceEventPayload) -> None:
-        raise RuntimeError("boom")
-
-    def good_callback(_payload: InstanceEventPayload) -> None:
-        received.append("good_callback")
-
-    event_bus.subscribe("instance.started", bad_callback)
-    event_bus.subscribe("instance.started", good_callback)
-
-    # Should not raise
-    await event_bus.publish("instance.started", sample_payload)
-
-    assert received == ["good_callback"]
-
-
-@pytest.mark.unit
-async def test_unsubscribe_removes_callback(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """After unsubscribing, the callback should not be called."""
-    received: list[str] = []
-
-    def callback(_payload: InstanceEventPayload) -> None:
-        received.append("callback")
-
-    unsubscribe = event_bus.subscribe("instance.started", callback)
-    unsubscribe()
-
-    await event_bus.publish("instance.started", sample_payload)
-
-    assert received == []
-
-
-@pytest.mark.unit
-async def test_publish_to_empty_subscriber_list(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """Publishing to an event type with no subscribers should not raise."""
-    await event_bus.publish("instance.started", sample_payload)
-
-
-@pytest.mark.unit
-async def test_async_subscriber_supported(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """Async callbacks should be awaited correctly."""
-    received: list[str] = []
-
-    async def async_callback(_payload: InstanceEventPayload) -> None:
-        await asyncio.sleep(0)
-        received.append("async_callback")
-
-    event_bus.subscribe("instance.started", async_callback)
-    await event_bus.publish("instance.started", sample_payload)
-
-    assert received == ["async_callback"]
-
-
-@pytest.mark.unit
-async def test_unsubscribe_all_clears_subscribers(
-    event_bus: InstanceEventBus,
-    sample_payload: InstanceEventPayload,
-) -> None:
-    """unsubscribe_all should remove all callbacks for an event type."""
-    received: list[str] = []
-
-    def callback(_payload: InstanceEventPayload) -> None:
-        received.append("callback")
-
-    event_bus.subscribe("instance.started", callback)
-    event_bus.unsubscribe_all("instance.started")
-
-    await event_bus.publish("instance.started", sample_payload)
-
-    assert received == []

apps/api/tests/unit/test_file_service.py

@@ -1,84 +0,0 @@
-"""Unit tests for FileService."""
-
-import os
-import tempfile
-
-import pytest
-
-from src.models.workspace import Workspace
-from src.services.file_service import FileService
-
-
-@pytest.fixture
-def temp_workspace():
-    """Create a temporary workspace directory."""
-    with tempfile.TemporaryDirectory() as tmpdir:
-        ws = Workspace(
-            id="00000000-0000-0000-0000-000000000001",
-            name="test-ws",
-            repo_id="00000000-0000-0000-0000-000000000002",
-            user_id="00000000-0000-0000-0000-000000000003",
-            branch="main",
-            path=tmpdir,
-        )
-        yield ws
-
-
-class TestFileService:
-    """Tests for FileService."""
-
-    def test_list_directory_empty(self, temp_workspace: Workspace):
-        """Returns empty list for empty directory."""
-        service = FileService()
-        entries = service.list_directory(temp_workspace)
-        assert entries == []
-
-    def test_list_directory_with_files(self, temp_workspace: Workspace):
-        """Returns entries sorted (dirs first, then files)."""
-        # Create files and dirs
-        os.makedirs(os.path.join(temp_workspace.path, "src"))
-        with open(os.path.join(temp_workspace.path, "README.md"), "w") as f:
-            f.write("# Test")
-        with open(os.path.join(temp_workspace.path, "main.py"), "w") as f:
-            f.write("print('hello')")
-
-        service = FileService()
-        entries = service.list_directory(temp_workspace)
-
-        assert len(entries) == 3
-        assert entries[0].name == "src" and entries[0].type == "directory"
-        assert entries[1].name == "main.py" and entries[1].type == "file"
-        assert entries[2].name == "README.md" and entries[2].type == "file"
-
-    def test_read_file(self, temp_workspace: Workspace):
-        """Reads text file content."""
-        with open(os.path.join(temp_workspace.path, "test.txt"), "w") as f:
-            f.write("hello world")
-
-        service = FileService()
-        content = service.read_file(temp_workspace, "test.txt")
-        assert content == "hello world"
-
-    def test_read_binary_file_rejected(self, temp_workspace: Workspace):
-        """Rejects binary files."""
-        with open(os.path.join(temp_workspace.path, "binary.bin"), "wb") as f:
-            f.write(b"\x00\x01\x02")
-
-        service = FileService()
-        with pytest.raises(ValueError, match="Binary"):
-            service.read_file(temp_workspace, "binary.bin")
-
-    def test_write_file(self, temp_workspace: Workspace):
-        """Writes file to workspace."""
-        service = FileService()
-        service.write_file(temp_workspace, "nested/file.txt", "content")
-
-        assert os.path.exists(os.path.join(temp_workspace.path, "nested", "file.txt"))
-        with open(os.path.join(temp_workspace.path, "nested", "file.txt")) as f:
-            assert f.read() == "content"
-
-    def test_path_escapes_workspace(self, temp_workspace: Workspace):
-        """Rejects paths that escape workspace directory."""
-        service = FileService()
-        with pytest.raises(ValueError, match="escapes"):
-            service.list_directory(temp_workspace, "../outside")

apps/api/tests/unit/test_git_mount_resolution.py

@@ -1,124 +0,0 @@
-"""Unit tests for git mount resolution in tool instances."""
-
-import os
-from pathlib import Path
-
-import pytest
-
-from src.api.tool_instances import (
-    _checkout_branch,
-    _expand_glob_source,
-    _resolve_single_git_mount,
-)
-
-
-class TestExpandGlobSource:
-    """Unit tests for glob pattern expansion."""
-
-    def test_no_glob_single_file(self, tmp_path: Path) -> None:
-        """Test non-glob path returns single file."""
-        test_file = tmp_path / "test.txt"
-        test_file.write_text("content")
-        
-        result = _expand_glob_source(str(test_file), str(tmp_path))
-        assert len(result) == 1
-        assert result[0] == str(test_file)
-
-    def test_no_glob_missing_file(self, tmp_path: Path) -> None:
-        """Test non-glob missing file returns empty list."""
-        missing_file = tmp_path / "missing.txt"
-        
-        result = _expand_glob_source(str(missing_file), str(tmp_path))
-        assert len(result) == 0
-
-    def test_glob_pattern(self, tmp_path: Path) -> None:
-        """Test glob pattern matches files."""
-        (tmp_path / "file1.txt").write_text("content1")
-        (tmp_path / "file2.txt").write_text("content2")
-        (tmp_path / "other.py").write_text("code")
-        
-        result = _expand_glob_source(str(tmp_path / "*.txt"), str(tmp_path))
-        assert len(result) == 2
-        assert all(f.endswith(".txt") for f in result)
-
-    def test_glob_recursive(self, tmp_path: Path) -> None:
-        """Test recursive glob pattern."""
-        subdir = tmp_path / "subdir"
-        subdir.mkdir()
-        (subdir / "nested.txt").write_text("content")
-        
-        result = _expand_glob_source(str(tmp_path / "**" / "*.txt"), str(tmp_path))
-        assert len(result) == 1
-        assert "nested.txt" in result[0]
-
-    def test_glob_limit_enforced(self, tmp_path: Path) -> None:
-        """Test that glob matches are limited to prevent abuse."""
-        # Create more than 100 files
-        for i in range(105):
-            (tmp_path / f"file{i}.txt").write_text("content")
-        
-        result = _expand_glob_source(str(tmp_path / "*.txt"), str(tmp_path))
-        assert len(result) == 100  # MAX_GLOB_MATCHES limit
-
-    def test_glob_escapes_repo(self, tmp_path: Path) -> None:
-        """Test that glob results outside repo are filtered."""
-        other_dir = tmp_path.parent / "other"
-        other_dir.mkdir(exist_ok=True)
-        (other_dir / "outside.txt").write_text("content")
-        
-        result = _expand_glob_source(str(tmp_path.parent / "*" / "*.txt"), str(tmp_path))
-        # Should only include files within tmp_path, not other_dir
-        assert all(r.startswith(str(tmp_path)) for r in result)
-
-
-class TestCheckoutBranch:
-    """Unit tests for branch checkout."""
-
-    def test_checkout_existing_branch(self, tmp_path: Path) -> None:
-        """Test checking out an existing branch."""
-        # Initialize git repo
-        os.system(f"cd {tmp_path} && git init && git config user.email 'test@test.com' && git config user.name 'Test'")
-        (tmp_path / "file.txt").write_text("content")
-        os.system(f"cd {tmp_path} && git add . && git commit -m 'initial'")
-        os.system(f"cd {tmp_path} && git branch feature")
-        
-        _checkout_branch(str(tmp_path), "feature")
-        
-        # Verify we're on feature branch
-        result = os.popen(f"cd {tmp_path} && git branch --show-current").read().strip()
-        assert result == "feature"
-
-    def test_checkout_nonexistent_branch(self, tmp_path: Path) -> None:
-        """Test checking out a non-existent branch returns False."""
-        os.system(f"cd {tmp_path} && git init && git config user.email 'test@test.com' && git config user.name 'Test'")
-        (tmp_path / "file.txt").write_text("content")
-        os.system(f"cd {tmp_path} && git add . && git commit -m 'initial'")
-        
-        result = _checkout_branch(str(tmp_path), "nonexistent")
-        assert result is False
-
-
-class TestResolveSingleGitMount:
-    """Unit tests for resolving a single git mount."""
-
-    @pytest.mark.asyncio
-    async def test_resolve_missing_remote_url(self, db_session) -> None:
-        """Test that missing remote_url returns empty list."""
-        git_mount = {
-            "source_path": ".",
-            "target_path": "/app",
-        }
-        
-        result = await _resolve_single_git_mount(db_session, git_mount)
-        assert result == []
-
-    @pytest.mark.asyncio
-    async def test_resolve_missing_target_path(self, db_session) -> None:
-        """Test that missing target path returns empty list."""
-        git_mount = {
-            "remote_url": "https://github.com/user/repo.git",
-            "source_path": ".",
-        }
-        
-        result = await _resolve_single_git_mount(db_session, git_mount)
-        assert result == []

apps/api/tests/unit/test_git_mounts.py

@@ -1,219 +0,0 @@
-"""Unit tests for git mount resolution with multi-mapping support."""
-
-import os
-import tempfile
-from unittest.mock import MagicMock, patch
-
-import pytest
-
-from src.api.tool_instances import (
-    _clone_git_repo,
-    _expand_glob_source,
-    _normalize_git_mount,
-    _resolve_git_mount_mappings,
-    _resolve_single_git_mount,
-)
-
-
-class TestNormalizeGitMount:
-    """Tests for _normalize_git_mount."""
-
-    def test_legacy_to_mappings(self) -> None:
-        """Legacy source_path + target_path becomes mappings array."""
-        entry = {
-            "remote_url": "https://github.com/user/repo.git",
-            "source_path": "packages/api",
-            "target_path": "/app/api",
-            "branch": "main",
-        }
-        result = _normalize_git_mount(entry)
-        assert "mappings" in result
-        assert result["mappings"] == [
-            {"source_path": "packages/api", "target_path": "/app/api"}
-        ]
-        assert "source_path" not in result
-        assert "target_path" not in result
-        assert result["remote_url"] == "https://github.com/user/repo.git"
-        assert result["branch"] == "main"
-
-    def test_already_mappings(self) -> None:
-        """Entry already with mappings is left unchanged."""
-        entry = {
-            "remote_url": "https://github.com/user/repo.git",
-            "branch": "main",
-            "mappings": [
-                {"source_path": "a", "target_path": "/a"},
-                {"source_path": "b", "target_path": "/b"},
-            ],
-        }
-        result = _normalize_git_mount(entry)
-        assert result["mappings"] == [
-            {"source_path": "a", "target_path": "/a"},
-            {"source_path": "b", "target_path": "/b"},
-        ]
-        assert "source_path" not in result
-        assert "target_path" not in result
-
-    def test_missing_target_path_no_mappings(self) -> None:
-        """Entry with source_path but no target_path creates empty mappings."""
-        entry = {
-            "remote_url": "https://github.com/user/repo.git",
-            "source_path": "src",
-        }
-        result = _normalize_git_mount(entry)
-        assert "mappings" not in result
-
-
-class TestResolveGitMountMappings:
-    """Tests for _resolve_git_mount_mappings."""
-
-    def test_single_mapping(self) -> None:
-        """A single mapping produces one volume mount."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            os.makedirs(os.path.join(repo_path, "packages", "api"))
-            mappings = [
-                {"source_path": "packages/api", "target_path": "/app/api"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, None)
-            assert len(result) == 1
-            assert result[0]["source"] == os.path.join(repo_path, "packages", "api")
-            assert result[0]["target"] == "/app/api"
-            assert result[0]["type"] == "bind"
-
-    def test_multiple_mappings(self) -> None:
-        """Multiple mappings from same repo produce multiple mounts."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            os.makedirs(os.path.join(repo_path, "packages", "api"))
-            os.makedirs(os.path.join(repo_path, "packages", "web"))
-            mappings = [
-                {"source_path": "packages/api", "target_path": "/app/api"},
-                {"source_path": "packages/web", "target_path": "/app/web"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, None)
-            assert len(result) == 2
-            targets = {r["target"] for r in result}
-            assert targets == {"/app/api", "/app/web"}
-
-    def test_relative_target_path(self) -> None:
-        """Relative target_path is resolved against working_directory."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            os.makedirs(os.path.join(repo_path, "src"))
-            mappings = [
-                {"source_path": "src", "target_path": "code"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, "/workspace")
-            assert len(result) == 1
-            assert result[0]["target"] == "/workspace/code"
-
-    def test_glob_expansion(self) -> None:
-        """Glob patterns in source_path are expanded."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            os.makedirs(os.path.join(repo_path, "packages", "api"))
-            os.makedirs(os.path.join(repo_path, "packages", "web"))
-            mappings = [
-                {"source_path": "packages/*", "target_path": "/app/packages"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, None)
-            assert len(result) == 2
-            targets = {r["target"] for r in result}
-            assert targets == {
-                os.path.join("/app/packages", "packages", "api"),
-                os.path.join("/app/packages", "packages", "web"),
-            }
-
-    def test_missing_target_path_skipped(self) -> None:
-        """Mapping without target_path is skipped."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            mappings = [
-                {"source_path": "src"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, None)
-            assert len(result) == 0
-
-    def test_no_working_directory_for_relative_target(self) -> None:
-        """Relative target without working_directory is skipped."""
-        with tempfile.TemporaryDirectory() as repo_path:
-            os.makedirs(os.path.join(repo_path, "src"))
-            mappings = [
-                {"source_path": "src", "target_path": "code"},
-            ]
-            result = _resolve_git_mount_mappings(repo_path, mappings, None)
-            assert len(result) == 0
-
-
-class TestResolveSingleGitMount:
-    """Tests for _resolve_single_git_mount."""
-
-    @pytest.mark.asyncio
-    async def test_missing_remote_url(self) -> None:
-        """Git mount without remote_url returns empty list."""
-        result = await _resolve_single_git_mount(
-            MagicMock(),
-            {"mappings": [{"source_path": ".", "target_path": "/app"}]},
-            "/tmp",
-            None,
-        )
-        assert result == []
-
-    @pytest.mark.asyncio
-    async def test_missing_instance_dir(self) -> None:
-        """Git mount without instance_dir returns empty list."""
-        result = await _resolve_single_git_mount(
-            MagicMock(),
-            {
-                "remote_url": "https://github.com/user/repo.git",
-                "mappings": [{"source_path": ".", "target_path": "/app"}],
-            },
-            None,
-            None,
-        )
-        assert result == []
-
-    @pytest.mark.asyncio
-    async def test_legacy_format_normalized(self) -> None:
-        """Legacy format is normalized and resolved."""
-        with tempfile.TemporaryDirectory() as instance_dir:
-            with patch(
-                "src.api.tool_instances._clone_git_repo",
-                return_value=os.path.join(instance_dir, "repo-clone"),
-            ):
-                os.makedirs(os.path.join(instance_dir, "repo-clone", "src"))
-                result = await _resolve_single_git_mount(
-                    MagicMock(),
-                    {
-                        "remote_url": "https://github.com/user/repo.git",
-                        "source_path": "src",
-                        "target_path": "/app/src",
-                    },
-                    instance_dir,
-                    None,
-                )
-                assert len(result) == 1
-                assert result[0]["target"] == "/app/src"
-
-
-class TestExpandGlobSource:
-    """Tests for _expand_glob_source."""
-
-    def test_no_glob(self) -> None:
-        """Non-glob path returns single item if exists."""
-        with tempfile.TemporaryDirectory() as tmp:
-            path = os.path.join(tmp, "file.txt")
-            open(path, "w").close()
-            result = _expand_glob_source(path, tmp)
-            assert result == [path]
-
-    def test_no_glob_missing(self) -> None:
-        """Non-glob path that doesn't exist returns empty list."""
-        with tempfile.TemporaryDirectory() as tmp:
-            path = os.path.join(tmp, "missing.txt")
-            result = _expand_glob_source(path, tmp)
-            assert result == []
-
-    def test_glob_pattern(self) -> None:
-        """Glob pattern expands to matched paths."""
-        with tempfile.TemporaryDirectory() as tmp:
-            open(os.path.join(tmp, "a.txt"), "w").close()
-            open(os.path.join(tmp, "b.txt"), "w").close()
-            result = _expand_glob_source(os.path.join(tmp, "*.txt"), tmp)
-            assert len(result) == 2

apps/api/tests/unit/test_git_service.py

@@ -1,155 +0,0 @@
-"""Unit tests for GitService."""
-
-import asyncio
-from unittest.mock import AsyncMock, MagicMock, patch
-
-import pytest
-
-from src.services.git_service import GitService
-
-
-class TestGitServiceClone:
-    """Tests for GitService.clone."""
-
-    @pytest.mark.asyncio
-    async def test_clone_success(self):
-        """Clone succeeds when git returns 0."""
-        mock_proc = AsyncMock()
-        mock_proc.returncode = 0
-        mock_proc.communicate.return_value = (b"", b"")
-
-        with patch(
-            "asyncio.create_subprocess_exec", return_value=mock_proc
-        ) as mock_exec:
-            await GitService.clone(
-                "https://github.com/test/repo.git", "main", "/tmp/ws"
-            )
-
-        mock_exec.assert_called_once_with(
-            "git",
-            "clone",
-            "--branch",
-            "main",
-            "--single-branch",
-            "https://github.com/test/repo.git",
-            "/tmp/ws",
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-
-    @pytest.mark.asyncio
-    async def test_clone_failure(self):
-        """Clone raises RuntimeError when git fails."""
-        mock_proc = AsyncMock()
-        mock_proc.returncode = 1
-        mock_proc.communicate.return_value = (b"", b"fatal: repository not found")
-
-        with patch("asyncio.create_subprocess_exec", return_value=mock_proc):
-            with pytest.raises(RuntimeError, match="Git clone failed"):
-                await GitService.clone("https://bad/url.git", "main", "/tmp/ws")
-
-
-class TestGitServiceFetch:
-    """Tests for GitService.fetch."""
-
-    @pytest.mark.asyncio
-    async def test_fetch_success(self):
-        """Fetch succeeds when git returns 0."""
-        mock_proc = AsyncMock()
-        mock_proc.returncode = 0
-        mock_proc.communicate.return_value = (b"", b"")
-
-        with patch(
-            "asyncio.create_subprocess_exec", return_value=mock_proc
-        ) as mock_exec:
-            await GitService.fetch("/tmp/repo")
-
-        mock_exec.assert_called_once_with(
-            "git",
-            "-C",
-            "/tmp/repo",
-            "fetch",
-            "origin",
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-
-    @pytest.mark.asyncio
-    async def test_fetch_failure(self):
-        """Fetch raises RuntimeError when git fails."""
-        mock_proc = AsyncMock()
-        mock_proc.returncode = 128
-        mock_proc.communicate.return_value = (b"", b"fatal: not a git repository")
-
-        with patch("asyncio.create_subprocess_exec", return_value=mock_proc):
-            with pytest.raises(RuntimeError, match="Git fetch failed"):
-                await GitService.fetch("/not/a/repo")
-
-
-class TestGitServicePull:
-    """Tests for GitService.pull."""
-
-    @pytest.mark.asyncio
-    async def test_pull_success(self):
-        """Pull succeeds when git returns 0."""
-        mock_proc = AsyncMock()
-        mock_proc.returncode = 0
-        mock_proc.communicate.return_value = (b"Already up to date.", b"")
-
-        with patch(
-            "asyncio.create_subprocess_exec", return_value=mock_proc
-        ) as mock_exec:
-            await GitService.pull("/tmp/repo", "feature-branch")
-
-        mock_exec.assert_called_once_with(
-            "git",
-            "-C",
-            "/tmp/repo",
-            "pull",
-            "origin",
-            "feature-branch",
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-
-
-class TestGitServiceBranchExistsRemotely:
-    """Tests for GitService.branch_exists_remotely."""
-
-    def test_branch_exists(self):
-        """Returns True when branch exists on remote."""
-        mock_result = MagicMock()
-        mock_result.returncode = 0
-        mock_result.stdout = "abc123 refs/heads/main\n"
-
-        with patch("subprocess.run", return_value=mock_result) as mock_run:
-            result = GitService.branch_exists_remotely("/tmp/repo", "main")
-
-        assert result is True
-        mock_run.assert_called_once_with(
-            ["git", "-C", "/tmp/repo", "ls-remote", "--heads", "origin", "main"],
-            capture_output=True,
-            text=True,
-        )
-
-    def test_branch_not_exists(self):
-        """Returns False when branch does not exist on remote."""
-        mock_result = MagicMock()
-        mock_result.returncode = 0
-        mock_result.stdout = ""
-
-        with patch("subprocess.run", return_value=mock_result):
-            result = GitService.branch_exists_remotely("/tmp/repo", "deleted-branch")
-
-        assert result is False
-
-    def test_ls_remote_fails(self):
-        """Returns False when ls-remote fails."""
-        mock_result = MagicMock()
-        mock_result.returncode = 128
-        mock_result.stdout = ""
-
-        with patch("subprocess.run", return_value=mock_result):
-            result = GitService.branch_exists_remotely("/tmp/repo", "main")
-
-        assert result is False

apps/api/tests/unit/test_health_monitor.py

@@ -1,292 +0,0 @@
-"""Unit tests for HealthMonitor state-transition logic."""
-
-import asyncio
-import uuid
-from contextlib import suppress
-from unittest.mock import patch
-
-import pytest
-from sqlalchemy import select
-
-from src.models.health_check import HealthCheck
-from src.models.tool_instance import ToolInstance
-from src.models.user import User
-from src.services.event_bus import InstanceEventBus, InstanceEventPayload
-from src.services.health_monitor import HealthMonitor, HealthSnapshot
-
-
-@pytest.fixture
-def event_bus() -> InstanceEventBus:
-    """Provide a fresh EventBus instance."""
-    bus = InstanceEventBus()
-    bus._reset_for_testing()
-    return bus
-
-
-@pytest.fixture
-def health_monitor(event_bus: InstanceEventBus) -> HealthMonitor:
-    """Provide a HealthMonitor with a short poll interval for testing."""
-    monitor = HealthMonitor(event_bus)
-    monitor.POLL_INTERVAL_SECONDS = 0.1
-    return monitor
-
-
-async def _create_running_instance(db_session) -> ToolInstance:
-    """Helper to create a user and a running tool instance."""
-    user = User(
-        id=uuid.uuid4(),
-        email="hm@example.com",
-        name="HM Test",
-        authentik_id="auth-hm",
-    )
-    db_session.add(user)
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="hm-test-instance",
-        display_name="HM Test Instance",
-        tool_type_id=uuid.uuid4(),
-        repository_id=uuid.uuid4(),
-        project_id=uuid.uuid4(),
-        owner_id=user.id,
-        status="running",
-        container_id="container123",
-        public_url="https://example.trycloudflare.com",
-    )
-    db_session.add(instance)
-    await db_session.commit()
-    return instance
-
-
-@pytest.mark.unit
-async def test_detects_container_crash(
-    db_session,
-    event_bus: InstanceEventBus,
-    health_monitor: HealthMonitor,
-) -> None:
-    """Monitor should detect exited container and publish error event."""
-    instance = await _create_running_instance(db_session)
-
-    events_captured: list[InstanceEventPayload] = []
-
-    def capture_event(payload: InstanceEventPayload) -> None:
-        events_captured.append(payload)
-
-    event_bus.subscribe("instance.error", capture_event)
-
-    with (
-        patch(
-            "src.services.health_monitor.get_container_status",
-            return_value={"status": "exited", "exit_code": 137, "health": None},
-        ),
-        patch(
-            "src.services.health_monitor.check_tunnel_health",
-            return_value={"healthy": False, "tunnel_status": "not_applicable"},
-        ),
-    ):
-        await health_monitor._check_instance(db_session, instance)
-
-    # Refresh instance from DB
-    await db_session.refresh(instance)
-    assert instance.status == "error"
-
-    # Event published
-    assert len(events_captured) == 1
-    assert events_captured[0]["event"] == "instance.error"
-    assert events_captured[0]["status"] == "error"
-    assert events_captured[0]["metadata"]["exit_code"] == 137
-
-    # Health check row inserted
-    result = await db_session.execute(
-        select(HealthCheck).where(HealthCheck.instance_id == instance.id)
-    )
-    check = result.scalar_one()
-    assert check.container_status == "exited"
-    assert check.exit_code == 137
-
-
-@pytest.mark.unit
-async def test_detects_tunnel_failure(
-    db_session,
-    event_bus: InstanceEventBus,
-    health_monitor: HealthMonitor,
-) -> None:
-    """Monitor should detect tunnel failure and mark unhealthy."""
-    instance = await _create_running_instance(db_session)
-
-    events_captured: list[InstanceEventPayload] = []
-
-    def capture_event(payload: InstanceEventPayload) -> None:
-        events_captured.append(payload)
-
-    event_bus.subscribe("instance.health_changed", capture_event)
-
-    with (
-        patch(
-            "src.services.health_monitor.get_container_status",
-            return_value={"status": "running", "exit_code": None, "health": "healthy"},
-        ),
-        patch(
-            "src.services.health_monitor.check_tunnel_health",
-            return_value={
-                "healthy": False,
-                "tunnel_status": "error_response",
-                "status_code": 502,
-            },
-        ),
-    ):
-        await health_monitor._check_instance(db_session, instance)
-
-    await db_session.refresh(instance)
-    assert instance.status == "unhealthy"
-
-    assert len(events_captured) == 1
-    assert events_captured[0]["event"] == "instance.health_changed"
-    assert events_captured[0]["status"] == "unhealthy"
-    assert events_captured[0]["metadata"]["previous_status"] == "running"
-
-    result = await db_session.execute(
-        select(HealthCheck).where(HealthCheck.instance_id == instance.id)
-    )
-    check = result.scalar_one()
-    assert check.tunnel_healthy is False
-
-
-@pytest.mark.unit
-async def test_detects_recovery(
-    db_session,
-    event_bus: InstanceEventBus,
-    health_monitor: HealthMonitor,
-) -> None:
-    """Monitor should detect recovery from unhealthy to running."""
-    instance = await _create_running_instance(db_session)
-    instance.status = "unhealthy"
-    await db_session.commit()
-
-    # Seed last known state as unhealthy
-    health_monitor._last_known_state[instance.id] = HealthSnapshot(
-        container_status="running",
-        container_healthy=None,
-        tunnel_healthy=False,
-        exit_code=None,
-    )
-
-    events_captured: list[InstanceEventPayload] = []
-
-    def capture_event(payload: InstanceEventPayload) -> None:
-        events_captured.append(payload)
-
-    event_bus.subscribe("instance.health_changed", capture_event)
-
-    with (
-        patch(
-            "src.services.health_monitor.get_container_status",
-            return_value={"status": "running", "exit_code": None, "health": None},
-        ),
-        patch(
-            "src.services.health_monitor.check_tunnel_health",
-            return_value={
-                "healthy": True,
-                "tunnel_status": "healthy",
-                "status_code": 200,
-            },
-        ),
-    ):
-        await health_monitor._check_instance(db_session, instance)
-
-    await db_session.refresh(instance)
-    assert instance.status == "running"
-
-    assert len(events_captured) == 1
-    assert events_captured[0]["status"] == "running"
-    assert events_captured[0]["metadata"]["previous_status"] == "unhealthy"
-
-    result = await db_session.execute(
-        select(HealthCheck).where(HealthCheck.instance_id == instance.id)
-    )
-    check = result.scalar_one()
-    assert check.tunnel_healthy is True
-
-
-@pytest.mark.unit
-async def test_skips_writes_when_no_state_change(
-    db_session,
-    event_bus: InstanceEventBus,
-    health_monitor: HealthMonitor,
-) -> None:
-    """Two identical polls should result in only one health_checks row."""
-    instance = await _create_running_instance(db_session)
-
-    with (
-        patch(
-            "src.services.health_monitor.get_container_status",
-            return_value={"status": "running", "exit_code": None, "health": None},
-        ),
-        patch(
-            "src.services.health_monitor.check_tunnel_health",
-            return_value={
-                "healthy": True,
-                "tunnel_status": "healthy",
-                "status_code": 200,
-            },
-        ),
-    ):
-        await health_monitor._check_instance(db_session, instance)
-        await health_monitor._check_instance(db_session, instance)
-
-    result = await db_session.execute(
-        select(HealthCheck).where(HealthCheck.instance_id == instance.id)
-    )
-    assert len(result.scalars().all()) == 1
-
-
-@pytest.mark.unit
-async def test_docker_exception_resilience(
-    db_session,
-    event_bus: InstanceEventBus,
-    health_monitor: HealthMonitor,
-) -> None:
-    """Docker exception should be caught and not propagate."""
-    instance = await _create_running_instance(db_session)
-
-    events_captured: list[InstanceEventPayload] = []
-
-    def capture_event(payload: InstanceEventPayload) -> None:
-        events_captured.append(payload)
-
-    event_bus.subscribe("instance.error", capture_event)
-    event_bus.subscribe("instance.health_changed", capture_event)
-
-    with patch(
-        "src.services.health_monitor.get_container_status",
-        side_effect=RuntimeError("docker exploded"),
-    ):
-        # Should not raise
-        await health_monitor._check_instance(db_session, instance)
-
-    # No DB writes
-    result = await db_session.execute(
-        select(HealthCheck).where(HealthCheck.instance_id == instance.id)
-    )
-    assert result.scalar_one_or_none() is None
-
-    # No events published
-    assert events_captured == []
-
-
-@pytest.mark.unit
-async def test_monitor_start_stop(health_monitor: HealthMonitor) -> None:
-    """Start and stop should manage the background task."""
-    health_monitor.start()
-    task = health_monitor._task
-    assert task is not None
-    assert not task.done()
-
-    health_monitor.stop()
-    if task is not None and not task.done():
-        with suppress(asyncio.CancelledError):
-            await task
-    assert task is not None
-    assert task.cancelled() or task.done()
-    assert health_monitor._last_known_state == {}

apps/api/tests/unit/test_home_path_expansion.py

@@ -1,110 +0,0 @@
-"""Unit tests for ~ / $HOME expansion in container paths."""
-
-import pytest
-
-from src.api.tool_instances import _resolve_git_mount_mappings
-from src.services.config_profile_resolver import expand_container_path
-from src.services.manifest_compiler import get_manifest_home_dir
-
-
-class TestExpandContainerPath:
-    """Tests for expand_container_path helper."""
-
-    def test_tilde_slash_expands(self) -> None:
-        """~/foo should expand to home_dir/foo."""
-        assert (
-            expand_container_path("~/workspace", "/home/user") == "/home/user/workspace"
-        )
-
-    def test_tilde_alone_expands(self) -> None:
-        """~ should expand to home_dir."""
-        assert expand_container_path("~", "/home/user") == "/home/user"
-
-    def test_dollar_home_slash_expands(self) -> None:
-        """$HOME/foo should expand to home_dir/foo."""
-        assert (
-            expand_container_path("$HOME/workspace", "/home/user")
-            == "/home/user/workspace"
-        )
-
-    def test_dollar_home_alone_expands(self) -> None:
-        """$HOME should expand to home_dir."""
-        assert expand_container_path("$HOME", "/home/user") == "/home/user"
-
-    def test_absolute_path_unchanged(self) -> None:
-        """Absolute paths should not be modified."""
-        assert expand_container_path("/app/workspace", "/home/user") == "/app/workspace"
-
-    def test_relative_path_unchanged(self) -> None:
-        """Relative paths should not be modified."""
-        assert expand_container_path("workspace", "/home/user") == "workspace"
-
-    def test_tilde_in_middle_unchanged(self) -> None:
-        """~ in the middle of a path should not expand."""
-        assert expand_container_path("/app/~user", "/home/user") == "/app/~user"
-
-    def test_dollar_home_in_middle_unchanged(self) -> None:
-        """$HOME in the middle of a path should not expand."""
-        assert expand_container_path("/app/$HOMEuser", "/home/user") == "/app/$HOMEuser"
-
-    def test_root_home(self) -> None:
-        """Expansion works with /root as home."""
-        assert expand_container_path("~/config", "/root") == "/root/config"
-
-
-class TestGetManifestHomeDir:
-    """Tests for get_manifest_home_dir helper."""
-
-    def test_with_user_block(self) -> None:
-        """Manifest with user block returns /home/{name}."""
-        manifest = {"user": {"name": "developer", "uid": 1000, "gid": 1000}}
-        assert get_manifest_home_dir(manifest) == "/home/developer"
-
-    def test_without_user_block(self) -> None:
-        """Manifest without user block returns /root."""
-        manifest = {"base_image": "ubuntu:24.04"}
-        assert get_manifest_home_dir(manifest) == "/root"
-
-    def test_with_empty_user_name(self) -> None:
-        """Manifest with empty user name returns /root."""
-        manifest = {"user": {"name": "", "uid": 1000, "gid": 1000}}
-        assert get_manifest_home_dir(manifest) == "/root"
-
-    def test_with_none_user_name(self) -> None:
-        """Manifest with None user name returns /root."""
-        manifest = {"user": {"name": None, "uid": 1000, "gid": 1000}}
-        assert get_manifest_home_dir(manifest) == "/root"
-
-
-class TestResolveGitMountMappingsExpansion:
-    """Tests that git mount mapping targets expand ~ and $HOME."""
-
-    def test_tilde_target_expansion(self, tmp_path) -> None:
-        """Mapping with ~/repo target expands to home dir."""
-        (tmp_path / "src").mkdir()
-        mappings = [{"source_path": "src", "target_path": "~/repo"}]
-        result = _resolve_git_mount_mappings(
-            str(tmp_path), mappings, None, "/home/user"
-        )
-        assert len(result) == 1
-        assert result[0]["target"] == "/home/user/repo"
-
-    def test_dollar_home_target_expansion(self, tmp_path) -> None:
-        """Mapping with $HOME/repo target expands to home dir."""
-        (tmp_path / "src").mkdir()
-        mappings = [{"source_path": "src", "target_path": "$HOME/repo"}]
-        result = _resolve_git_mount_mappings(
-            str(tmp_path), mappings, None, "/home/user"
-        )
-        assert len(result) == 1
-        assert result[0]["target"] == "/home/user/repo"
-
-    def test_absolute_target_unchanged(self, tmp_path) -> None:
-        """Absolute target paths are not modified."""
-        (tmp_path / "src").mkdir()
-        mappings = [{"source_path": "src", "target_path": "/app/src"}]
-        result = _resolve_git_mount_mappings(
-            str(tmp_path), mappings, None, "/home/user"
-        )
-        assert len(result) == 1
-        assert result[0]["target"] == "/app/src"

apps/api/tests/unit/test_lifecycle_hooks.py

@@ -1,49 +0,0 @@
-"""Unit tests for lifecycle hook helpers."""
-
-import pytest
-
-from src.services.lifecycle_hooks import _derive_title, _should_notify
-
-
-class TestDeriveTitle:
-    """Tests for _derive_title."""
-
-    def test_known_event_types(self) -> None:
-        assert _derive_title("instance.created") == "Container created"
-        assert _derive_title("instance.started") == "Container started"
-        assert _derive_title("instance.stopped") == "Container stopped"
-        assert _derive_title("instance.restarted") == "Container restarted"
-        assert _derive_title("instance.deleted") == "Container deleted"
-        assert _derive_title("instance.error") == "Container error"
-        assert _derive_title("instance.health_changed") == "Container ready"
-
-    def test_unknown_event_type(self) -> None:
-        assert _derive_title("instance.custom_event") == "Custom Event"
-
-
-class TestShouldNotify:
-    """Tests for _should_notify filtering."""
-
-    def test_error_events_are_notified(self) -> None:
-        assert _should_notify("instance.error", "error") is True
-        assert _should_notify("instance.error", None) is True
-
-    def test_health_changed_running_is_notified(self) -> None:
-        assert _should_notify("instance.health_changed", "running") is True
-
-    def test_created_started_stopped_restarted_deleted_filtered(self) -> None:
-        for event in [
-            "instance.created",
-            "instance.started",
-            "instance.stopped",
-            "instance.restarted",
-            "instance.deleted",
-        ]:
-            assert _should_notify(event, "pending") is False
-            assert _should_notify(event, "running") is False
-            assert _should_notify(event, None) is False
-
-    def test_health_changed_non_running_filtered(self) -> None:
-        assert _should_notify("instance.health_changed", "unhealthy") is False
-        assert _should_notify("instance.health_changed", "starting") is False
-        assert _should_notify("instance.health_changed", None) is False

apps/api/tests/unit/test_manifest_compiler.py

@@ -1,365 +0,0 @@
-"""Unit tests for the manifest compiler."""
-
-import pytest
-
-from src.services.manifest_compiler import (
-    compile_compose,
-    compile_dockerfile,
-    compile_entrypoint,
-    compute_image_tag,
-    deep_merge,
-    get_manifest_home_dir,
-    merge_with_config,
-    resolve_base,
-)
-
-
-class TestResolveBase:
-    """Tests for resolve_base."""
-
-    def test_returns_manifest_unchanged_when_no_base(self) -> None:
-        manifest = {"name": "test", "base_image": "ubuntu:24.04"}
-        result = resolve_base(manifest)
-        assert result["name"] == "test"
-        assert "base_definition_id" not in result
-
-
-class TestDeepMerge:
-    """Tests for deep_merge."""
-
-    def test_packages_are_unioned(self) -> None:
-        base = {"packages": {"apt": ["curl", "git"]}}
-        override = {"packages": {"apt": ["neovim"]}}
-        result = deep_merge(base, override)
-        assert result["packages"]["apt"] == ["curl", "git", "neovim"]
-
-    def test_node_version_overrides(self) -> None:
-        base = {"packages": {"node": {"version": "18"}}}
-        override = {"packages": {"node": {"version": "20"}}}
-        result = deep_merge(base, override)
-        assert result["packages"]["node"]["version"] == "20"
-
-    def test_env_is_merged_with_override_winning(self) -> None:
-        base = {"env": {"FOO": "base", "BAR": "base"}}
-        override = {"env": {"FOO": "override"}}
-        result = deep_merge(base, override)
-        assert result["env"]["FOO"] == "override"
-        assert result["env"]["BAR"] == "base"
-
-    def test_build_scripts_are_concatenated(self) -> None:
-        base = {"scripts": {"build": ["echo base"]}}
-        override = {"scripts": {"build": ["echo override"]}}
-        result = deep_merge(base, override)
-        assert result["scripts"]["build"] == ["echo base", "echo override"]
-
-    def test_mounts_are_concatenated(self) -> None:
-        base = {"mounts": [{"name": "base-mount", "target": "/base"}]}
-        override = {"mounts": [{"name": "tool-mount", "target": "/tool"}]}
-        result = deep_merge(base, override)
-        assert len(result["mounts"]) == 2
-
-    def test_user_is_overridden_entirely(self) -> None:
-        base = {"user": {"name": "base", "uid": 1000}}
-        override = {"user": {"name": "tool", "uid": 1001}}
-        result = deep_merge(base, override)
-        assert result["user"]["name"] == "tool"
-        assert result["user"]["uid"] == 1001
-
-
-class TestCompileDockerfile:
-    """Tests for compile_dockerfile."""
-
-    def test_includes_from(self) -> None:
-        manifest = {"base_image": "ubuntu:24.04", "name": "test"}
-        df = compile_dockerfile(manifest)
-        assert "FROM ubuntu:24.04" in df
-
-    def test_installs_apt_packages(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "packages": {"apt": ["curl", "git"]},
-        }
-        df = compile_dockerfile(manifest)
-        assert "apt-get install -y" in df
-        assert "curl" in df
-        assert "git" in df
-        assert "rm -rf /var/lib/apt/lists/*" in df
-
-    def test_installs_node(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "packages": {"node": {"version": "20"}},
-        }
-        df = compile_dockerfile(manifest)
-        assert "nodesource.com/setup_20.x" in df
-
-    def test_installs_npm_global(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "packages": {"npm_global": ["@scope/pkg"]},
-        }
-        df = compile_dockerfile(manifest)
-        assert "npm install -g @scope/pkg" in df
-
-    def test_creates_user(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "user": {"name": "dev", "uid": 1001, "gid": 1001},
-        }
-        df = compile_dockerfile(manifest)
-        assert "groupadd -g 1001 dev" in df
-        assert "useradd -u 1001 -g 1001" in df
-        assert "USER dev" in df
-
-    def test_build_scripts_as_run_commands(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "scripts": {"build": ["echo hello", "echo world"]},
-        }
-        df = compile_dockerfile(manifest)
-        assert "RUN echo hello" in df
-        assert "RUN echo world" in df
-
-    def test_creates_mount_directories(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "user": {"name": "dev", "uid": 1001, "gid": 1001},
-            "mounts": [
-                {"name": "ws", "target": "/workspace"},
-                {"name": "cfg", "target": "/config"},
-            ],
-        }
-        df = compile_dockerfile(manifest)
-        assert "mkdir -p /workspace /config" in df
-        assert "chown -R dev:dev /workspace /config" in df
-
-    def test_entrypoint_for_startup_scripts(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "scripts": {"startup": ["echo start"]},
-        }
-        df = compile_dockerfile(manifest)
-        assert 'ENTRYPOINT ["/usr/local/bin/headquarter-entrypoint"]' in df
-
-    def test_cmd_from_runtime(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "runtime": {"command": ["/bin/bash", "-il"]},
-        }
-        df = compile_dockerfile(manifest)
-        assert 'CMD ["/bin/bash", "-il"]' in df
-
-    def test_default_cmd_when_no_runtime(self) -> None:
-        manifest = {"base_image": "ubuntu:24.04", "name": "test"}
-        df = compile_dockerfile(manifest)
-        assert 'CMD ["/bin/bash"]' in df
-
-    def test_sets_home_env_for_user(self) -> None:
-        manifest = {
-            "base_image": "ubuntu:24.04",
-            "name": "test",
-            "user": {"name": "dev", "uid": 1001, "gid": 1001},
-        }
-        df = compile_dockerfile(manifest)
-        assert "ENV HOME=/home/dev" in df
-        assert "ENV USER=dev" in df
-
-    def test_no_home_env_without_user(self) -> None:
-        manifest = {"base_image": "ubuntu:24.04", "name": "test"}
-        df = compile_dockerfile(manifest)
-        assert "ENV HOME=" not in df
-        assert "ENV USER=" not in df
-
-
-class TestGetManifestHomeDir:
-    """Tests for get_manifest_home_dir."""
-
-    def test_with_user_name(self) -> None:
-        manifest = {"user": {"name": "dev", "uid": 1001, "gid": 1001}}
-        assert get_manifest_home_dir(manifest) == "/home/dev"
-
-    def test_without_user(self) -> None:
-        manifest = {"base_image": "ubuntu:24.04"}
-        assert get_manifest_home_dir(manifest) == "/root"
-
-    def test_with_empty_user_name(self) -> None:
-        manifest = {"user": {"name": "", "uid": 1001, "gid": 1001}}
-        assert get_manifest_home_dir(manifest) == "/root"
-
-
-class TestCompileEntrypoint:
-    """Tests for compile_entrypoint."""
-
-    def test_includes_shebang_and_set_e(self) -> None:
-        manifest = {"scripts": {"startup": ["echo hello"]}}
-        ep = compile_entrypoint(manifest)
-        assert "#!/bin/bash" in ep
-        assert "set -e" in ep
-
-    def test_includes_startup_scripts(self) -> None:
-        manifest = {"scripts": {"startup": ["echo hello", "echo world"]}}
-        ep = compile_entrypoint(manifest)
-        assert "echo hello" in ep
-        assert "echo world" in ep
-
-    def test_ends_with_exec(self) -> None:
-        manifest: dict = {"scripts": {"startup": []}}
-        ep = compile_entrypoint(manifest)
-        assert 'exec "$@"' in ep
-
-
-class TestCompileCompose:
-    """Tests for compile_compose."""
-
-    def test_includes_image_and_container_name(self) -> None:
-        manifest = {"name": "test", "interface_type": "terminal"}
-        vars_dict = {"IMAGE_TAG": "test:v1", "INSTANCE_NAME": "test-1"}
-        compose = compile_compose(manifest, vars_dict)
-        assert "image: test:v1" in compose
-        assert "container_name: test-1" in compose
-
-    def test_terminal_fields(self) -> None:
-        manifest = {
-            "name": "test",
-            "interface_type": "terminal",
-            "runtime": {"stdin_open": True, "tty": True, "working_dir": "/workspace"},
-        }
-        compose = compile_compose(manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n"})
-        assert "stdin_open: true" in compose
-        assert "tty: true" in compose
-        assert "working_dir: /workspace" in compose
-
-    def test_web_ports(self) -> None:
-        manifest = {
-            "name": "test",
-            "interface_type": "web",
-            "default_port": 8080,
-        }
-        compose = compile_compose(
-            manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n", "TOOL_PORT": "3000"}
-        )
-        assert "3000:8080" in compose
-
-    def test_user_override(self) -> None:
-        manifest = {
-            "name": "test",
-            "interface_type": "terminal",
-            "user": {"uid": 1001, "gid": 1001},
-        }
-        compose = compile_compose(manifest, {"IMAGE_TAG": "t", "INSTANCE_NAME": "n"})
-        assert "user: 1001:1001" in compose
-
-    def test_mounts_resolved(self) -> None:
-        manifest = {
-            "name": "test",
-            "interface_type": "terminal",
-            "mounts": [
-                {"name": "ws", "target": "/workspace", "source_type": "repo"},
-                {
-                    "name": "ssh",
-                    "target": "/home/user/.ssh",
-                    "source_type": "ssh_key",
-                    "readonly": True,
-                },
-            ],
-        }
-        compose = compile_compose(
-            manifest,
-            {
-                "IMAGE_TAG": "t",
-                "INSTANCE_NAME": "n",
-                "REPO_PATH": "/repos/myrepo",
-                "SSH_PATH": "/keys/ssh",
-            },
-        )
-        assert "/repos/myrepo:/workspace" in compose
-        assert "/keys/ssh:/home/user/.ssh:ro" in compose
-
-    def test_extra_volumes_appended(self) -> None:
-        manifest = {"name": "test", "interface_type": "terminal"}
-        compose = compile_compose(
-            manifest,
-            {
-                "IMAGE_TAG": "t",
-                "INSTANCE_NAME": "n",
-                "EXTRA_VOLUMES": [{"source": "/host/x", "target": "/container/x"}],
-            },
-        )
-        assert "/host/x:/container/x" in compose
-
-
-class TestComputeImageTag:
-    """Tests for compute_image_tag."""
-
-    def test_is_deterministic(self) -> None:
-        manifest = {"name": "test", "packages": {"apt": ["curl"]}}
-        tag1 = compute_image_tag("My Tool", manifest)
-        tag2 = compute_image_tag("My Tool", manifest)
-        assert tag1 == tag2
-
-    def test_changes_with_content(self) -> None:
-        manifest1 = {"name": "test", "packages": {"apt": ["curl"]}}
-        manifest2 = {"name": "test", "packages": {"apt": ["wget"]}}
-        tag1 = compute_image_tag("test", manifest1)
-        tag2 = compute_image_tag("test", manifest2)
-        assert tag1 != tag2
-
-    def test_lowercases_name(self) -> None:
-        manifest = {"name": "test"}
-        tag = compute_image_tag("My Tool", manifest)
-        assert "my-tool" in tag
-
-    def test_valid_docker_reference(self) -> None:
-        manifest = {"name": "test"}
-        tag = compute_image_tag("test", manifest)
-        assert tag.startswith("headquarter/test-")
-        assert tag.endswith(":latest")
-
-
-class TestMergeWithConfig:
-    """Tests for merge_with_config (ConfigProfile only)."""
-
-    def test_no_profile_returns_manifest_unchanged(self) -> None:
-        manifest = {"name": "test"}
-        result = merge_with_config(manifest)
-        assert result["name"] == "test"
-        assert result["_extra_env"] == {}
-        assert result["_extra_volumes"] == []
-
-    def test_profile_env_vars(self) -> None:
-        manifest = {"name": "test"}
-        profile = {"environment_variables": {"FOO": "bar"}}
-        result = merge_with_config(manifest, profile)
-        assert result["_extra_env"]["FOO"] == "bar"
-
-    def test_profile_mounts(self) -> None:
-        manifest = {"name": "test"}
-        profile = {"mounts": [{"source": "/host", "target": "/container"}]}
-        result = merge_with_config(manifest, profile)
-        assert len(result["_extra_volumes"]) == 1
-
-    def test_profile_port_override(self) -> None:
-        manifest = {"name": "test", "default_port": 8080}
-        profile = {"hints": {"port_override": 3000}}
-        result = merge_with_config(manifest, profile)
-        assert result["default_port"] == 3000
-
-    def test_profile_start_command(self) -> None:
-        manifest = {"name": "test", "runtime": {"command": ["/bin/bash"]}}
-        profile = {"hints": {"start_command": "/bin/sh"}}
-        result = merge_with_config(manifest, profile)
-        assert result["runtime"]["command"] == ["/bin/sh"]
-
-    def test_profile_working_directory(self) -> None:
-        manifest = {"name": "test"}
-        profile = {"hints": {"working_directory": "/workspace"}}
-        result = merge_with_config(manifest, profile)
-        assert result["runtime"]["working_dir"] == "/workspace"

apps/api/tests/unit/test_monitoring_models.py

@@ -1,143 +0,0 @@
-"""Unit tests for monitoring models and migration compatibility."""
-
-import uuid
-from datetime import datetime
-
-import pytest
-from sqlalchemy import select
-
-from src.models.health_check import HealthCheck
-from src.models.instance_event import InstanceEvent
-from src.models.tool_instance import ToolInstance
-from src.models.user import User
-
-
-@pytest.mark.unit
-async def test_instance_event_creation(db_session) -> None:
-    """InstanceEvent model can be created and persisted."""
-    user = User(
-        id=uuid.uuid4(),
-        email="test@example.com",
-        name="Test",
-        authentik_id="auth-1",
-    )
-    db_session.add(user)
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance",
-        display_name="Test Instance",
-        tool_type_id=uuid.uuid4(),
-        repository_id=uuid.uuid4(),
-        project_id=uuid.uuid4(),
-        owner_id=user.id,
-        status="pending",
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    event = InstanceEvent(
-        instance_id=instance.id,
-        event_type="started",
-        status="starting",
-        message="Container starting...",
-        created_by=user.id,
-        event_metadata={"previous_status": "pending"},
-    )
-    db_session.add(event)
-    await db_session.commit()
-    await db_session.refresh(event)
-
-    assert event.id is not None
-    assert event.instance_id == instance.id
-    assert event.event_type == "started"
-    assert event.status == "starting"
-    assert event.created_by == user.id
-    assert event.event_metadata == {"previous_status": "pending"}
-    assert isinstance(event.created_at, datetime)
-
-
-@pytest.mark.unit
-async def test_health_check_creation(db_session) -> None:
-    """HealthCheck model can be created and persisted."""
-    user = User(
-        id=uuid.uuid4(),
-        email="test2@example.com",
-        name="Test2",
-        authentik_id="auth-2",
-    )
-    db_session.add(user)
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance-2",
-        display_name="Test Instance 2",
-        tool_type_id=uuid.uuid4(),
-        repository_id=uuid.uuid4(),
-        project_id=uuid.uuid4(),
-        owner_id=user.id,
-        status="running",
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    check = HealthCheck(
-        instance_id=instance.id,
-        container_status="running",
-        container_healthy=True,
-        tunnel_healthy=True,
-        exit_code=None,
-        probe_status="passed",
-        probe_output="OK",
-    )
-    db_session.add(check)
-    await db_session.commit()
-    await db_session.refresh(check)
-
-    assert check.id is not None
-    assert check.instance_id == instance.id
-    assert check.container_status == "running"
-    assert check.container_healthy is True
-    assert check.tunnel_healthy is True
-    assert isinstance(check.checked_at, datetime)
-
-
-@pytest.mark.unit
-async def test_instance_event_query_by_instance(db_session) -> None:
-    """InstanceEvent rows can be queried by instance_id."""
-    user = User(
-        id=uuid.uuid4(),
-        email="test3@example.com",
-        name="Test3",
-        authentik_id="auth-3",
-    )
-    db_session.add(user)
-    await db_session.commit()
-
-    instance = ToolInstance(
-        id=uuid.uuid4(),
-        name="test-instance-3",
-        display_name="Test Instance 3",
-        tool_type_id=uuid.uuid4(),
-        repository_id=uuid.uuid4(),
-        project_id=uuid.uuid4(),
-        owner_id=user.id,
-        status="pending",
-    )
-    db_session.add(instance)
-    await db_session.commit()
-
-    event = InstanceEvent(
-        instance_id=instance.id,
-        event_type="created",
-        status="pending",
-    )
-    db_session.add(event)
-    await db_session.commit()
-
-    result = await db_session.execute(
-        select(InstanceEvent).where(InstanceEvent.instance_id == instance.id)
-    )
-    assert result.scalar_one() is not None

apps/api/tests/unit/test_notification_service.py

@@ -1,387 +0,0 @@
-"""Unit tests for NotificationService."""
-
-import uuid
-from datetime import datetime, timedelta, timezone
-
-import pytest
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.models.notification import Notification
-from src.models.user import User
-from src.services.notification_service import NotificationService
-
-
-@pytest.fixture
-def notification_service() -> NotificationService:
-    return NotificationService()
-
-
-@pytest.fixture
-async def user_a(db_session: AsyncSession) -> User:
-    user = User(
-        id=uuid.uuid4(),
-        email="user-a@headquarter.local",
-        name="User A",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(user)
-    await db_session.commit()
-    return user
-
-
-@pytest.fixture
-async def user_b(db_session: AsyncSession) -> User:
-    user = User(
-        id=uuid.uuid4(),
-        email="user-b@headquarter.local",
-        name="User B",
-        authentik_id=f"authentik-{uuid.uuid4()}",
-        avatar_url=None,
-    )
-    db_session.add(user)
-    await db_session.commit()
-    return user
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_create_notification(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    notification = await notification_service.create_notification(
-        db_session,
-        user_a.id,
-        category="instance",
-        severity="info",
-        title="Container started",
-        message="Instance is running",
-        source_type="tool_instances",
-        source_id=uuid.uuid4(),
-        metadata={"key": "value"},
-    )
-
-    assert notification.user_id == user_a.id
-    assert notification.category == "instance"
-    assert notification.severity == "info"
-    assert notification.title == "Container started"
-    assert notification.message == "Instance is running"
-    assert notification.source_type == "tool_instances"
-    assert notification.notification_metadata == {"key": "value"}
-    assert notification.read_at is None
-    assert notification.dismissed_at is None
-    assert notification.created_at is not None
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_list_notifications_orders_by_created_at_desc(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n1 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="First"
-    )
-    n1.created_at = datetime.now(timezone.utc) - timedelta(seconds=2)
-    await db_session.commit()
-    await db_session.refresh(n1)
-
-    n2 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Second"
-    )
-    n2.created_at = datetime.now(timezone.utc) - timedelta(seconds=1)
-    await db_session.commit()
-    await db_session.refresh(n2)
-
-    n3 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Third"
-    )
-
-    items, total = await notification_service.list_notifications(db_session, user_a.id)
-
-    assert total == 3
-    assert [item.id for item in items] == [n3.id, n2.id, n1.id]
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_list_notifications_excludes_dismissed(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n1 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Visible"
-    )
-    n2 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Dismissed"
-    )
-    await notification_service.dismiss(db_session, n2.id, user_a.id)
-
-    items, total = await notification_service.list_notifications(db_session, user_a.id)
-
-    assert total == 1
-    assert items[0].id == n1.id
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_list_notifications_unread_only(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n1 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Unread"
-    )
-    n2 = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Read"
-    )
-    await notification_service.mark_read(db_session, n2.id, user_a.id)
-
-    items, total = await notification_service.list_notifications(
-        db_session, user_a.id, unread_only=True
-    )
-
-    assert total == 1
-    assert items[0].id == n1.id
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_get_unread_count(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    for i in range(5):
-        n = await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title=f"Notification {i}",
-        )
-        if i >= 3:
-            await notification_service.mark_read(db_session, n.id, user_a.id)
-
-    count = await notification_service.get_unread_count(db_session, user_a.id)
-
-    assert count == 3
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_mark_read_sets_read_at(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Unread"
-    )
-
-    updated = await notification_service.mark_read(db_session, n.id, user_a.id)
-
-    assert updated.read_at is not None
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_mark_all_read_affects_all_unread(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    for i in range(4):
-        await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title=f"Notification {i}",
-        )
-
-    marked = await notification_service.mark_all_read(db_session, user_a.id)
-
-    assert marked == 4
-    count = await notification_service.get_unread_count(db_session, user_a.id)
-    assert count == 0
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_dismiss_sets_dismissed_at(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="To dismiss"
-    )
-
-    await notification_service.dismiss(db_session, n.id, user_a.id)
-
-    result = await db_session.execute(
-        select(Notification).where(Notification.id == n.id)
-    )
-    row = result.scalar_one()
-    assert row.dismissed_at is not None
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_mark_read_wrong_owner_raises(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    n = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Owned by A"
-    )
-
-    with pytest.raises(ValueError, match="Notification not found"):
-        await notification_service.mark_read(db_session, n.id, user_b.id)
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_dismiss_wrong_owner_raises(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    n = await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Owned by A"
-    )
-
-    with pytest.raises(ValueError, match="Notification not found"):
-        await notification_service.dismiss(db_session, n.id, user_b.id)
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_list_notifications_mute_categories(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    await notification_service.create_notification(
-        db_session, user_a.id, category="instance", severity="info", title="Instance"
-    )
-    n2 = await notification_service.create_notification(
-        db_session, user_a.id, category="system", severity="info", title="System"
-    )
-
-    items, total = await notification_service.list_notifications(
-        db_session, user_a.id, mute_categories=["instance"]
-    )
-
-    assert total == 1
-    assert items[0].id == n2.id
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_get_unread_count_excludes_dismissed(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    n = await notification_service.create_notification(
-        db_session,
-        user_a.id,
-        category="instance",
-        severity="info",
-        title="Unread dismissed",
-    )
-    await notification_service.dismiss(db_session, n.id, user_a.id)
-
-    count = await notification_service.get_unread_count(db_session, user_a.id)
-
-    assert count == 0
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_dismiss_all_affects_all_non_dismissed(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-) -> None:
-    for i in range(4):
-        await notification_service.create_notification(
-            db_session,
-            user_a.id,
-            category="instance",
-            severity="info",
-            title=f"Notification {i}",
-        )
-
-    cleared = await notification_service.dismiss_all(db_session, user_a.id)
-
-    assert cleared == 4
-    items, total = await notification_service.list_notifications(db_session, user_a.id)
-    assert total == 0
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_dismiss_all_affects_only_caller(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    for i in range(3):
-        await notification_service.create_notification(
-            db_session, user_a.id, category="instance", severity="info", title=f"A-{i}"
-        )
-    for i in range(2):
-        await notification_service.create_notification(
-            db_session, user_b.id, category="instance", severity="info", title=f"B-{i}"
-        )
-
-    cleared = await notification_service.dismiss_all(db_session, user_a.id)
-
-    assert cleared == 3
-    items_a, total_a = await notification_service.list_notifications(
-        db_session, user_a.id
-    )
-    items_b, total_b = await notification_service.list_notifications(
-        db_session, user_b.id
-    )
-    assert total_a == 0
-    assert total_b == 2
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio
-async def test_mark_all_read_affects_only_caller(
-    db_session: AsyncSession,
-    notification_service: NotificationService,
-    user_a: User,
-    user_b: User,
-) -> None:
-    for i in range(3):
-        await notification_service.create_notification(
-            db_session, user_a.id, category="instance", severity="info", title=f"A-{i}"
-        )
-    for i in range(2):
-        await notification_service.create_notification(
-            db_session, user_b.id, category="instance", severity="info", title=f"B-{i}"
-        )
-
-    marked = await notification_service.mark_all_read(db_session, user_a.id)
-
-    assert marked == 3
-    count_a = await notification_service.get_unread_count(db_session, user_a.id)
-    count_b = await notification_service.get_unread_count(db_session, user_b.id)
-    assert count_a == 0
-    assert count_b == 2

apps/api/tests/unit/test_notifications_api_routes.py

@@ -1,34 +0,0 @@
-"""Unit tests for notification API route ordering."""
-
-from fastapi import FastAPI
-from fastapi.testclient import TestClient
-
-from src.api.notifications import router as notifications_router
-
-
-def test_delete_notifications_route_order() -> None:
-    """DELETE /notifications must match before DELETE /notifications/{id}.
-
-    FastAPI matches routes in declaration order. The bulk clear endpoint
-    (DELETE /notifications) must be registered before the single dismiss
-    endpoint (DELETE /notifications/{notification_id}) or the path
-    parameter route will intercept the bulk route.
-    """
-    app = FastAPI()
-    app.include_router(notifications_router)
-    client = TestClient(app)
-
-    # Verify the bulk delete route exists and returns the expected schema
-    # (it will 401 without auth, but that's fine — we just need to confirm
-    # routing doesn't hit the UUID-parameter route first)
-    response = client.delete("/notifications")
-    # Should get 401 (unauthenticated), NOT 422 (UUID parse error)
-    assert response.status_code == 401, (
-        f"Expected 401 (auth required), got {response.status_code}. "
-        f"Route order may be wrong — DELETE /notifications matched "
-        f"DELETE /notifications/{{notification_id}} instead."
-    )
-
-    # Verify the single dismiss route still works (also 401 without auth)
-    response = client.delete("/notifications/12345678-1234-1234-1234-123456789abc")
-    assert response.status_code == 401

apps/api/tests/unit/test_permission_fixer.py

@@ -1,237 +0,0 @@
-"""Unit tests for the permission fixer."""
-
-from unittest.mock import MagicMock, patch
-
-import pytest
-
-from src.services.permission_fixer import (
-    PermissionFixError,
-    apply_mount_permissions,
-    apply_ssh_permissions,
-    check_root_user_available,
-    _run_in_container,
-)
-
-
-class TestApplyMountPermissions:
-    """Tests for apply_mount_permissions."""
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_applies_chown_when_owner_declared(self, mock_run) -> None:
-        mounts = [
-            {"name": "workspace", "target": "/workspace", "owner": "user"},
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert len(results) == 1
-        assert results[0]["mount_name"] == "workspace"
-        assert results[0]["success"] is True
-        mock_run.assert_called_once()
-        args = mock_run.call_args[0]
-        assert args[0] == "abc123"
-        assert args[1] == ["chown", "-R", "user:user", "/workspace"]
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_applies_chmod_when_mode_declared(self, mock_run) -> None:
-        mounts = [
-            {"name": "ssh", "target": "/home/user/.ssh", "mode": "0700"},
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert results[0]["success"] is True
-        # Only chmod called (no owner, so no chown)
-        assert mock_run.call_count == 1
-        chmod_call = mock_run.call_args_list[0]
-        assert chmod_call[0][1] == ["chmod", "0700", "/home/user/.ssh"]
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_applies_file_mode_when_declared(self, mock_run) -> None:
-        mounts = [
-            {
-                "name": "ssh",
-                "target": "/home/user/.ssh",
-                "file_mode": "0600",
-            },
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert results[0]["success"] is True
-        # Only file_mode called (no owner, no mode)
-        assert mock_run.call_count == 1
-        file_mode_call = mock_run.call_args_list[0]
-        assert file_mode_call[0][1][0] == "sh"
-        assert (
-            "find /home/user/.ssh -type f -exec chmod 0600" in file_mode_call[0][1][2]
-        )
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_skips_readonly_mount(self, mock_run) -> None:
-        mounts = [
-            {
-                "name": "ssh_keys",
-                "target": "/home/user/.ssh",
-                "readonly": True,
-                "mode": "0700",
-                "file_mode": "0600",
-            },
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert len(results) == 1
-        assert results[0]["mount_name"] == "ssh_keys"
-        assert results[0]["success"] is True
-        mock_run.assert_not_called()
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_skips_mount_with_no_policy(self, mock_run) -> None:
-        mounts = [
-            {"name": "workspace", "target": "/workspace", "writable": True},
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert len(results) == 1
-        assert results[0]["success"] is True
-        mock_run.assert_not_called()
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_reports_failure_on_command_error(self, mock_run) -> None:
-        mock_run.side_effect = PermissionFixError("chown failed")
-
-        mounts = [
-            {"name": "workspace", "target": "/workspace", "owner": "user"},
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert results[0]["success"] is False
-        assert "chown failed" in results[0]["error"]
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_stops_on_first_failure(self, mock_run) -> None:
-        """If chown fails, chmod and file_mode should not run."""
-        mock_run.side_effect = PermissionFixError("chown failed")
-
-        mounts = [
-            {
-                "name": "workspace",
-                "target": "/workspace",
-                "owner": "user",
-                "mode": "0755",
-                "file_mode": "0644",
-            },
-        ]
-        results = apply_mount_permissions("abc123", mounts)
-
-        assert results[0]["success"] is False
-        assert mock_run.call_count == 1  # Only chown attempted
-
-
-class TestRunInContainer:
-    """Tests for _run_in_container."""
-
-    @patch("subprocess.run")
-    def test_success(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=0, stderr="")
-        _run_in_container("abc123", ["echo", "hello"], 10)
-        mock_run.assert_called_once()
-        cmd = mock_run.call_args[0][0]
-        assert cmd == ["docker", "exec", "--user", "root", "abc123", "echo", "hello"]
-
-    @patch("subprocess.run")
-    def test_failure_raises(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=1, stderr="permission denied")
-        with pytest.raises(PermissionFixError, match="permission denied"):
-            _run_in_container("abc123", ["chown", "x"], 10)
-
-    @patch("subprocess.run")
-    def test_timeout_raises(self, mock_run) -> None:
-        import subprocess
-
-        mock_run.side_effect = subprocess.TimeoutExpired(cmd=["docker"], timeout=10)
-        with pytest.raises(PermissionFixError, match="timed out"):
-            _run_in_container("abc123", ["chown", "x"], 10)
-
-
-class TestApplySshPermissions:
-    """Tests for apply_ssh_permissions."""
-
-    @patch("subprocess.run")
-    def test_applies_chown_chmod_and_file_mode(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
-        result = apply_ssh_permissions("abc123", "/home/user/.ssh", "user")
-
-        assert result["success"] is True
-        # 3 fix commands + 3 verification commands
-        assert mock_run.call_count == 6
-        chown_cmd = mock_run.call_args_list[0][0][0]
-        chmod_cmd = mock_run.call_args_list[1][0][0]
-        file_mode_cmd = mock_run.call_args_list[2][0][0]
-
-        assert chown_cmd == [
-            "docker",
-            "exec",
-            "--user",
-            "root",
-            "abc123",
-            "chown",
-            "-R",
-            "user:user",
-            "/home/user/.ssh",
-        ]
-        assert chmod_cmd == [
-            "docker",
-            "exec",
-            "--user",
-            "root",
-            "abc123",
-            "chmod",
-            "700",
-            "/home/user/.ssh",
-        ]
-        assert file_mode_cmd[0] == "docker"
-        assert (
-            "find /home/user/.ssh -name 'id_*' -type f -exec chmod 600"
-            in file_mode_cmd[-1]
-        )
-
-    @patch("subprocess.run")
-    def test_uses_root_user(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
-        result = apply_ssh_permissions("abc123", "/root/.ssh", "root")
-
-        assert result["success"] is True
-        chown_cmd = mock_run.call_args_list[0][0][0]
-        assert chown_cmd == [
-            "docker",
-            "exec",
-            "--user",
-            "root",
-            "abc123",
-            "chown",
-            "-R",
-            "root:root",
-            "/root/.ssh",
-        ]
-
-    @patch("subprocess.run")
-    def test_reports_failure(self, mock_run) -> None:
-        mock_run.return_value = MagicMock(
-            returncode=1, stdout="", stderr="chown failed"
-        )
-
-        result = apply_ssh_permissions("abc123", "/home/user/.ssh", "user")
-
-        assert result["success"] is False
-        assert "chown failed" in result["error"]
-
-
-class TestCheckRootUserAvailable:
-    """Tests for check_root_user_available."""
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_returns_true_when_root_exists(self, mock_run) -> None:
-        assert check_root_user_available("abc123") is True
-
-    @patch("src.services.permission_fixer._run_in_container")
-    def test_returns_false_when_root_missing(self, mock_run) -> None:
-        mock_run.side_effect = PermissionFixError("no such user")
-        assert check_root_user_available("abc123") is False

apps/api/tests/unit/test_session_branch_selection.py

@@ -1,179 +0,0 @@
-"""Tests for session creation with branch selection and new branch creation."""
-
-import os
-import subprocess
-import tempfile
-
-
-from src.api.tool_instances import CreateInstanceRequest
-
-
-class TestCreateInstanceRequest:
-    """Tests for CreateInstanceRequest model."""
-
-    def test_default_values(self):
-        """Test default values for CreateInstanceRequest."""
-        request = CreateInstanceRequest(tool_type_id="123")
-        assert request.clone_mode == "mount"
-        assert request.branch == "main"
-        assert request.new_branch is None
-        assert request.display_name is None
-
-    def test_clone_mode_with_branch(self):
-        """Test CreateInstanceRequest with clone mode and branch."""
-        request = CreateInstanceRequest(
-            tool_type_id="123",
-            clone_mode="clone",
-            branch="dev",
-        )
-        assert request.clone_mode == "clone"
-        assert request.branch == "dev"
-
-    def test_new_branch_field(self):
-        """Test CreateInstanceRequest with new_branch field."""
-        request = CreateInstanceRequest(
-            tool_type_id="123",
-            clone_mode="clone",
-            branch="main",
-            new_branch="feature/test",
-        )
-        assert request.new_branch == "feature/test"
-
-
-class TestBranchCreationInClone:
-    """Tests for branch creation logic in clone process."""
-
-    def test_create_local_branch_success(self):
-        """Test successful local branch creation."""
-        with tempfile.TemporaryDirectory() as tmpdir:
-            # Initialize repo
-            subprocess.run(
-                ["git", "init", tmpdir],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create initial commit
-            readme = os.path.join(tmpdir, "README.md")
-            with open(readme, "w") as f:
-                f.write("# Test\n")
-            subprocess.run(
-                ["git", "-C", tmpdir, "add", "README.md"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create new branch
-            result = subprocess.run(
-                ["git", "-C", tmpdir, "checkout", "-b", "feature/new-branch"],
-                capture_output=True,
-                text=True,
-            )
-            
-            assert result.returncode == 0
-            
-            # Verify branch exists
-            branches_result = subprocess.run(
-                ["git", "-C", tmpdir, "branch", "--show-current"],
-                capture_output=True,
-                text=True,
-            )
-            assert branches_result.stdout.strip() == "feature/new-branch"
-
-    def test_create_local_branch_invalid_name(self):
-        """Test local branch creation with invalid name fails."""
-        with tempfile.TemporaryDirectory() as tmpdir:
-            # Initialize repo
-            subprocess.run(
-                ["git", "init", tmpdir],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.email", "test@test.com"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "config", "user.name", "Test User"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Create initial commit
-            readme = os.path.join(tmpdir, "README.md")
-            with open(readme, "w") as f:
-                f.write("# Test\n")
-            subprocess.run(
-                ["git", "-C", tmpdir, "add", "README.md"],
-                capture_output=True,
-                check=True,
-            )
-            subprocess.run(
-                ["git", "-C", tmpdir, "commit", "-m", "Initial commit"],
-                capture_output=True,
-                check=True,
-            )
-            
-            # Try to create branch with invalid name (contains spaces)
-            result = subprocess.run(
-                ["git", "-C", tmpdir, "checkout", "-b", "invalid branch name"],
-                capture_output=True,
-                text=True,
-            )
-            
-            # Git accepts branch names with spaces but it's not recommended
-            # This test verifies the command structure
-            assert result.returncode == 0 or "fatal" in result.stderr
-
-
-class TestCreateInstanceAPI:
-    """Tests for create instance API endpoint with branch options."""
-
-    def test_create_instance_request_validation(self):
-        """Test that CreateInstanceRequest validates correctly."""
-        # Valid request with new_branch
-        request = CreateInstanceRequest(
-            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
-            clone_mode="clone",
-            branch="main",
-            new_branch="feature/test",
-        )
-        assert request.new_branch == "feature/test"
-        
-        # Valid request without new_branch
-        request2 = CreateInstanceRequest(
-            tool_type_id="550e8400-e29b-41d4-a716-446655440000",
-            clone_mode="clone",
-            branch="dev",
-        )
-        assert request2.new_branch is None
-
-    def test_create_instance_with_new_branch_sets_instance_branch(self):
-        """Test that instance branch is set to new_branch when provided."""
-        # This tests the logic: data.new_branch if data.new_branch else data.branch
-        new_branch = "feature/test"
-        base_branch = "main"
-        
-        # Simulate the logic from create_instance
-        stored_branch = new_branch if new_branch else base_branch
-        assert stored_branch == "feature/test"
-        
-        # Without new_branch
-        stored_branch2 = None if None else base_branch
-        assert stored_branch2 == "main"

apps/api/tests/unit/test_ssh_keys.py

@@ -1,61 +0,0 @@
-"""Unit tests for SSH key preparation."""
-
-import os
-from pathlib import Path
-from unittest.mock import MagicMock, patch
-
-import pytest
-
-from src.services.ssh_keys import prepare_ssh_key_files
-
-
-class TestPrepareSshKeyFiles:
-    """Tests for prepare_ssh_key_files."""
-
-    @patch("src.services.ssh_keys._get_fernet")
-    def test_creates_files_with_default_permissions(
-        self, mock_fernet, tmp_path
-    ) -> None:
-        mock_fernet.return_value.decrypt.return_value = b"private-key-content"
-        ssh_key = MagicMock()
-        ssh_key.private_key_encrypted = "enc"
-        ssh_key.public_key = "ssh-ed25519 AAA test@test"
-
-        ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key)
-
-        assert Path(ssh_dir).exists()
-        assert (Path(ssh_dir) / "id_ed25519").exists()
-        assert (Path(ssh_dir) / "id_ed25519.pub").exists()
-        assert (Path(ssh_dir) / "config").exists()
-        assert oct(os.stat(Path(ssh_dir) / "id_ed25519").st_mode)[-3:] == "600"
-
-    @patch("src.services.ssh_keys._get_fernet")
-    def test_sets_ownership_when_uid_gid_provided(self, mock_fernet, tmp_path) -> None:
-        mock_fernet.return_value.decrypt.return_value = b"private-key-content"
-        ssh_key = MagicMock()
-        ssh_key.private_key_encrypted = "enc"
-        ssh_key.public_key = "ssh-ed25519 AAA test@test"
-
-        with patch("os.chown") as mock_chown:
-            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
-
-        # os.chown is called for the directory and each of the 3 files
-        assert mock_chown.call_count == 4
-        # First call is the directory
-        assert mock_chown.call_args_list[0][0][1] == 1001
-        assert mock_chown.call_args_list[0][0][2] == 1001
-
-    @patch("src.services.ssh_keys._get_fernet")
-    def test_gracefully_handles_permission_error_on_chown(
-        self, mock_fernet, tmp_path
-    ) -> None:
-        mock_fernet.return_value.decrypt.return_value = b"private-key-content"
-        ssh_key = MagicMock()
-        ssh_key.private_key_encrypted = "enc"
-        ssh_key.public_key = "ssh-ed25519 AAA test@test"
-
-        with patch("os.chown", side_effect=PermissionError("not allowed")):
-            # Should not raise
-            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
-
-        assert Path(ssh_dir).exists()

apps/web/.pi-lens/cache/tsx-rules-v2.json

@@ -1,36 +0,0 @@
-{
-  "version": "v2",
-  "timestamp": 1779892231625,
-  "ruleHash": "0a2423849fae7580",
-  "queries": [
-    {
-      "id": "dangerously-set-inner-html",
-      "name": "Dangerously Set Inner HTML",
-      "severity": "error",
-      "language": "tsx",
-      "message": "dangerouslySetInnerHTML — XSS risk, sanitize user input",
-      "query": "  (jsx_attribute\n    (property_identifier) @ATTR\n    (#match? @ATTR \"dangerouslySetInnerHTML\"))",
-      "metavars": [
-        "ATTR"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/tsx/dangerously-set-inner-html.yml"
-    },
-    {
-      "id": "no-nested-links",
-      "name": "Nested anchor tags",
-      "severity": "error",
-      "language": "tsx",
-      "message": "Nested <a> tags are invalid HTML and cause unexpected behavior",
-      "query": "  (jsx_element\n    open_tag: (jsx_opening_element\n      (identifier) @OUTER\n      (#eq? @OUTER \"a\"))\n    (jsx_element\n      open_tag: (jsx_opening_element\n        (identifier) @INNER\n        (#eq? @INNER \"a\"))))",
-      "metavars": [
-        "OUTER",
-        "INNER"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/tsx/no-nested-links.yml"
-    }
-  ]
-}

apps/web/.pi-lens/cache/typescript-rules-v2.json

@@ -1,477 +0,0 @@
-{
-  "version": "v2",
-  "timestamp": 1779889832502,
-  "ruleHash": "45ab8be323739a4e",
-  "queries": [
-    {
-      "id": "console-statement",
-      "name": "Console Statement",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "{{METHOD}} — remove debug statements before committing",
-      "query": "  (call_expression\n    function: (member_expression\n      object: (identifier) @OBJ (#eq? @OBJ \"console\")\n      property: (property_identifier) @METHOD (#not-eq? @METHOD \"dbg\"))\n    arguments: (arguments) @ARGS)",
-      "metavars": [
-        "OBJ",
-        "METHOD",
-        "ARGS"
-      ],
-      "post_filter": "not_in_test_block  # skip test blocks — no-console-in-tests handles that case",
-      "defect_class": "safety",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/console-statement.yml"
-    },
-    {
-      "id": "debugger-statement",
-      "name": "Debugger Statement",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Debugger statement — remove before committing",
-      "query": "  (debugger_statement) @DEBUGGER",
-      "metavars": [
-        "DEBUGGER"
-      ],
-      "defect_class": "safety",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/debugger.yml"
-    },
-    {
-      "id": "deep-nesting",
-      "name": "Deep Nesting",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Deep nesting (3+ levels) — consider early returns or extract functions",
-      "query": "  [\n    ;; Pattern 1: if inside if inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (if_statement\n            consequence: (statement_block\n              (if_statement) @IF_NESTED)))))\n\n    ;; Pattern 2: for inside if inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (if_statement\n            consequence: (statement_block\n              (for_statement) @FOR_NESTED)))))\n\n    ;; Pattern 3: while inside if inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (if_statement\n            consequence: (statement_block\n              (while_statement) @WHILE_NESTED)))))\n\n    ;; Pattern 4: try inside if inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (if_statement\n            consequence: (statement_block\n              (try_statement) @TRY_NESTED)))))\n\n    ;; Pattern 5: if inside for inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (for_statement\n            body: (statement_block\n              (if_statement) @IF_IN_FOR)))))\n\n    ;; Pattern 6: if inside while inside if\n    (statement_block\n      (if_statement\n        consequence: (statement_block\n          (while_statement\n            body: (statement_block\n              (if_statement) @IF_IN_WHILE)))))\n\n    ;; Pattern 7: for inside for inside for\n    (statement_block\n      (for_statement\n        body: (statement_block\n          (for_statement\n            body: (statement_block\n              (for_statement) @FOR_NESTED)))))\n  ]",
-      "metavars": [
-        "IF_NESTED",
-        "FOR_NESTED",
-        "WHILE_NESTED",
-        "TRY_NESTED",
-        "IF_IN_FOR",
-        "IF_IN_WHILE"
-      ],
-      "defect_class": "safety",
-      "inline_tier": "review",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/deep-nesting.yml"
-    },
-    {
-      "id": "deep-promise-chain",
-      "name": "Deep Promise Chain (4+ levels)",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Promise chain {{M1}} → {{M2}} → {{M3}} → {{M4}} — consider async/await",
-      "query": "  (call_expression\n    function: (member_expression\n      object: (call_expression\n        function: (member_expression\n          object: (call_expression\n            function: (member_expression\n              object: (call_expression\n                function: (member_expression\n                  property: (property_identifier) @M1)\n                arguments: (arguments))\n              property: (property_identifier) @M2)\n            arguments: (arguments))\n          property: (property_identifier) @M3)\n        arguments: (arguments))\n      property: (property_identifier) @M4)\n    arguments: (arguments)\n    (#match? @M1 \"^(then|catch|finally)$\")\n    (#match? @M2 \"^(then|catch|finally)$\")\n    (#match? @M3 \"^(then|catch|finally)$\")\n    (#match? @M4 \"^(then|catch|finally)$\"))",
-      "metavars": [
-        "M1",
-        "M2",
-        "M3",
-        "M4"
-      ],
-      "defect_class": "async-misuse",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/deep-promise-chain.yml"
-    },
-    {
-      "id": "default-not-last",
-      "name": "Default Clauses Should Be Last",
-      "severity": "error",
-      "language": "typescript",
-      "message": "default clause should be the last case",
-      "query": "  (switch_statement\n    body: (switch_body\n      (switch_default) @DEFAULT\n      (switch_case) @AFTER_CASE))",
-      "metavars": [
-        "DEFAULT",
-        "AFTER_CASE"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/default-not-last.yml"
-    },
-    {
-      "id": "duplicate-function-arg",
-      "name": "Function Argument Names Should Be Unique",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Duplicate parameter name '{{NAME}}'",
-      "query": "  (function_declaration\n    parameters: (formal_parameters\n      (identifier) @PARAM1\n      (identifier) @PARAM2))\n  (arrow_function\n    parameters: (formal_parameters\n      (identifier) @PARAM1\n      (identifier) @PARAM2))",
-      "metavars": [
-        "PARAM1",
-        "PARAM2"
-      ],
-      "post_filter": "same_param_name",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/duplicate-function-arg.yml"
-    },
-    {
-      "id": "empty-switch-case",
-      "name": "Switch Cases Should Not Be Empty",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Switch case should not be empty",
-      "query": "  (switch_statement\n    body: (switch_body\n      (switch_case\n        consequence: (statement_block) @BLOCK)))",
-      "metavars": [
-        "BLOCK"
-      ],
-      "post_filter": "is_empty_block",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/empty-switch-case.yml"
-    },
-    {
-      "id": "no-eval",
-      "name": "Eval Usage",
-      "severity": "error",
-      "language": "typescript",
-      "message": "eval() detected — security risk, never use eval",
-      "query": "  (call_expression\n    function: (identifier) @FUNC\n    (#eq? @FUNC \"eval\")\n    arguments: (arguments) @ARGS)",
-      "metavars": [
-        "FUNC",
-        "ARGS"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/eval.yml"
-    },
-    {
-      "id": "ts-incomplete-assertion",
-      "name": "Incomplete Test Assertion",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Incomplete assertion — expect() chain is not called",
-      "query": "  (call_expression\n    function: (identifier) @EXPECT\n    (#eq? @EXPECT \"expect\")\n    arguments: (arguments)) @EXPR",
-      "metavars": [
-        "EXPECT",
-        "EXPR"
-      ],
-      "post_filter": "incomplete_assertion",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/incomplete-assertion.yml"
-    },
-    {
-      "id": "infinite-loop",
-      "name": "Loops Should Not Be Infinite",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Loop appears to be infinite with no termination condition",
-      "query": "  (while_statement\n    condition: (true)\n    body: (statement_block) @BODY)\n  (for_statement\n    condition: (null)\n    body: (statement_block) @BODY)",
-      "metavars": [
-        "BODY"
-      ],
-      "post_filter": "no_break_or_return_in_body",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/infinite-loop.yml"
-    },
-    {
-      "id": "mixed-async-styles",
-      "name": "Mixed Async/Await and Promise Chains",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Mixed async/await + promise chains — use consistent async style",
-      "query": "  (function_declaration\n    (async_modifier)\n    body: (statement_block) @BODY)\n\n# Post-filter: Check if body contains both await and .then()",
-      "metavars": [
-        "BODY"
-      ],
-      "post_filter": "has_mixed_async",
-      "defect_class": "async-misuse",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/mixed-async-styles.yml"
-    },
-    {
-      "id": "no-console-in-tests",
-      "name": "Console Statement in Test",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "console.{{METHOD}} in test block — use proper assertions or logging",
-      "query": "  (call_expression\n    function: (member_expression\n      object: (identifier) @OBJ (#eq? @OBJ \"console\")\n      property: (property_identifier) @METHOD)\n    arguments: (arguments) @ARGS)",
-      "metavars": [
-        "OBJ",
-        "METHOD",
-        "ARGS"
-      ],
-      "post_filter": "in_test_block",
-      "defect_class": "safety",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/no-console-in-tests.yml"
-    },
-    {
-      "id": "self-assignment",
-      "name": "Variables Should Not Be Self-Assigned",
-      "severity": "error",
-      "language": "typescript",
-      "message": "'{{VAR}}' is assigned to itself",
-      "query": "  (assignment_expression\n    left: (identifier) @VAR\n    right: (identifier) @SAME\n    (#eq? @VAR @SAME))",
-      "metavars": [
-        "VAR",
-        "SAME"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/self-assignment.yml"
-    },
-    {
-      "id": "sql-injection",
-      "name": "SQL Injection Risk",
-      "severity": "error",
-      "language": "typescript",
-      "message": "SQL injection risk — use parameterized queries, never interpolate into SQL",
-      "query": "  (call_expression\n    function: [\n      (identifier) @SQL_FUNC\n      (member_expression property: (property_identifier) @SQL_FUNC)\n    ]\n    arguments: (arguments\n      (template_string (template_substitution) @INTERPOLATION))\n    (#match? @SQL_FUNC \"^(query|execute|exec|run)$\"))",
-      "metavars": [
-        "SQL_FUNC",
-        "INTERPOLATION"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/sql-injection.yml"
-    },
-    {
-      "id": "switch-case-termination",
-      "name": "Switch Cases Should End With Terminating Statement",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Switch case should end with break, return, throw, or continue",
-      "query": "  (switch_statement\n    body: (switch_body\n      (switch_case\n        consequence: (statement_block\n          (expression_statement) @LAST))\n      (switch_case) @NEXT))",
-      "metavars": [
-        "LAST",
-        "NEXT"
-      ],
-      "post_filter": "no_terminating_statement",
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/switch-case-termination.yml"
-    },
-    {
-      "id": "switch-non-case-labels-ts",
-      "name": "Switch Should Not Contain Non-Case Labels",
-      "severity": "error",
-      "language": "typescript",
-      "message": "switch statements should not contain non-case labels",
-      "query": "  (switch_statement\n    body: (switch_body\n      (switch_case\n        (labeled_statement\n          (statement_identifier) @LABEL) @LABELED)))",
-      "metavars": [
-        "LABEL",
-        "LABELED"
-      ],
-      "defect_class": "correctness",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/switch-non-case-labels.yml"
-    },
-    {
-      "id": "ts-command-injection",
-      "name": "Command Injection Sink",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Potential command injection sink — avoid child_process command execution with untrusted input",
-      "query": "  [\n    (call_expression\n      function: (member_expression\n        object: (identifier) @MOD\n        property: (property_identifier) @FN)\n      arguments: (arguments) @ARGS\n      (#eq? @MOD \"child_process\")\n      (#match? @FN \"^(exec|execSync)$\"))\n    (call_expression\n      function: (member_expression\n        object: (member_expression\n          object: (identifier) @MOD\n          property: (property_identifier) @NS)\n        property: (property_identifier) @FN)\n      arguments: (arguments) @ARGS\n      (#eq? @MOD \"child_process\")\n      (#match? @FN \"^(exec|execSync)$\"))\n  ]",
-      "metavars": [
-        "MOD",
-        "NS",
-        "FN",
-        "ARGS"
-      ],
-      "post_filter": "ts_command_injection_sink",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-command-injection.yml"
-    },
-    {
-      "id": "ts-detached-async-call",
-      "name": "Detached Async Call",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Detached async call — ensure this Promise is awaited or explicitly handled",
-      "query": "  (expression_statement\n    (call_expression\n      function: [\n        (identifier) @FN\n        (member_expression\n          property: (property_identifier) @FN)\n      ]\n      arguments: (arguments) @ARGS)\n    (#match? @FN \"(Async$|fetch$|request$)\"))",
-      "metavars": [
-        "FN",
-        "ARGS"
-      ],
-      "post_filter": "ts_detached_async_call",
-      "defect_class": "async-misuse",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-detached-async-call.yml"
-    },
-    {
-      "id": "ts-dynamic-require",
-      "name": "Dynamic Require Injection",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Dynamic require() — non-literal argument allows loading arbitrary modules",
-      "query": "  (call_expression\n    function: (identifier) @FN\n    arguments: (arguments [(identifier) (member_expression) (call_expression) (await_expression)] @ARG)\n    (#eq? @FN \"require\"))",
-      "metavars": [
-        "FN",
-        "ARG"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-dynamic-require.yml"
-    },
-    {
-      "id": "ts-hallucinated-react-import",
-      "name": "Hallucinated React Import",
-      "severity": "error",
-      "language": "typescript",
-      "message": "'{NAME}' is a Next.js API, not from 'react' — import from 'next/{CORRECT}' instead",
-      "query": "  (import_statement\n    (import_clause\n      (named_imports\n        (import_specifier\n          name: (identifier) @NAME)))\n    source: (string) @SRC)\n  (#match? @SRC \"^['\\\"]react['\\\"]$\")\n  (#match? @NAME \"^(useRouter|usePathname|useSearchParams|useParams|Link|Image|Script|Head|getServerSideProps|getStaticProps|getStaticPaths|NextPage|NextApiRequest|NextApiResponse|GetServerSideProps|GetStaticProps|GetStaticPaths|notFound|redirect|permanentRedirect)$\")",
-      "metavars": [
-        "NAME",
-        "SRC"
-      ],
-      "post_filter": "match_captures",
-      "post_filter_params": {
-        "SRC": "^['\\\"]react['\\\"]$",
-        "NAME": "^(useRouter|usePathname|useSearchParams|useParams|Link|Image|Script|Head|getServerSideProps|getStaticProps|getStaticPaths|NextPage|NextApiRequest|NextApiResponse|GetServerSideProps|GetStaticProps|GetStaticPaths|notFound|redirect|permanentRedirect)$"
-      },
-      "defect_class": "hallucination",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-hallucinated-react-import.yml"
-    },
-    {
-      "id": "ts-insecure-random",
-      "name": "Insecure Randomness",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Insecure randomness source detected — use crypto.getRandomValues or secure RNG APIs",
-      "query": "  (variable_declarator\n    name: (identifier) @VAR\n    value: (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments) @ARGS)\n    (#eq? @OBJ \"Math\")\n    (#eq? @FN \"random\")\n    (#match? @VAR \"(?i)(token|secret|password|key|nonce|salt|csrf|auth|session|credential|hash|otp|pin)\"))",
-      "metavars": [
-        "OBJ",
-        "FN",
-        "ARGS",
-        "VAR"
-      ],
-      "post_filter": "ts_insecure_random_source",
-      "defect_class": "injection",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-insecure-random.yml"
-    },
-    {
-      "id": "ts-nosql-injection",
-      "name": "NoSQL Injection",
-      "severity": "error",
-      "language": "typescript",
-      "message": "NoSQL injection — $where executes JavaScript server-side and must never be used with user input",
-      "query": "  (pair\n    key: [(property_identifier) (string)] @KEY\n    (#match? @KEY \"\\\\$where\"))",
-      "metavars": [
-        "KEY"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-nosql-injection.yml"
-    },
-    {
-      "id": "ts-open-redirect",
-      "name": "Open Redirect",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Open redirect — unvalidated URL in redirect/location lets attackers send users to malicious sites",
-      "query": "  [\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (identifier) @URL)\n      (#match? @OBJ \"^(res|response|ctx|context)$\")\n      (#eq? @FN \"redirect\"))\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (member_expression) @URL)\n      (#match? @OBJ \"^(res|response|ctx|context)$\")\n      (#eq? @FN \"redirect\"))\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (call_expression) @URL)\n      (#match? @OBJ \"^(res|response|ctx|context)$\")\n      (#eq? @FN \"redirect\"))\n  ]\n  [\n    (assignment_expression\n      left: (member_expression\n        object: (member_expression\n          object: (identifier) @WIN\n          property: (property_identifier) @LOC)\n        property: (property_identifier) @PROP)\n      right: (identifier) @VALUE\n      (#eq? @WIN \"window\")\n      (#eq? @LOC \"location\")\n      (#eq? @PROP \"href\"))\n    (assignment_expression\n      left: (member_expression\n        object: (member_expression\n          object: (identifier) @WIN\n          property: (property_identifier) @LOC)\n        property: (property_identifier) @PROP)\n      right: (member_expression) @VALUE\n      (#eq? @WIN \"window\")\n      (#eq? @LOC \"location\")\n      (#eq? @PROP \"href\"))\n    (assignment_expression\n      left: (member_expression\n        object: (member_expression\n          object: (identifier) @WIN\n          property: (property_identifier) @LOC)\n        property: (property_identifier) @PROP)\n      right: (call_expression) @VALUE\n      (#eq? @WIN \"window\")\n      (#eq? @LOC \"location\")\n      (#eq? @PROP \"href\"))\n  ]",
-      "metavars": [
-        "OBJ",
-        "FN",
-        "URL",
-        "WIN",
-        "LOC",
-        "PROP",
-        "VALUE"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-open-redirect.yml"
-    },
-    {
-      "id": "ts-react-antipatterns",
-      "name": "React Anti-Pattern",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "React anti-pattern: setState inside a loop causes multiple re-renders — batch with a single state update",
-      "query": "  [\n    (for_statement\n      (statement_block) @BODY\n      (#match? @BODY \"set[A-Z]\")\n      (#not-match? @BODY \"set(Timeout|Interval|Immediate)\"))\n    (for_in_statement\n      (statement_block) @BODY\n      (#match? @BODY \"set[A-Z]\")\n      (#not-match? @BODY \"set(Timeout|Interval|Immediate)\"))\n    (while_statement\n      (statement_block) @BODY\n      (#match? @BODY \"set[A-Z]\")\n      (#not-match? @BODY \"set(Timeout|Interval|Immediate)\"))\n  ]",
-      "metavars": [
-        "BODY"
-      ],
-      "defect_class": "logic-error",
-      "inline_tier": "warning",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-react-antipatterns.yml"
-    },
-    {
-      "id": "ts-ssrf",
-      "name": "SSRF Risk",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Potential SSRF sink — validate and allowlist outbound URLs",
-      "query": "  [\n    (call_expression\n      function: (identifier) @FN\n      arguments: (arguments [(identifier) (member_expression) (call_expression) (await_expression)] @URL)\n      (#match? @FN \"^(fetch|get|post|put|patch|delete|request)$\"))\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments [(identifier) (member_expression) (call_expression) (await_expression)] @URL)\n      (#match? @FN \"^(fetch|get|post|put|patch|delete|request)$\"))\n  ]",
-      "metavars": [
-        "OBJ",
-        "FN",
-        "URL"
-      ],
-      "post_filter": "ts_ssrf_sink",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-ssrf.yml"
-    },
-    {
-      "id": "ts-weak-hash",
-      "name": "Weak Hash Primitive",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Weak hash primitive selected (md5/sha1) — use sha256+ for security-sensitive contexts",
-      "query": "  (call_expression\n    function: (member_expression\n      property: (property_identifier) @FN)\n    arguments: (arguments\n      (string (string_fragment) @ALG)\n      (_)*)\n    (#eq? @FN \"createHash\")\n    (#match? @ALG \"^(md5|sha1)$\"))",
-      "metavars": [
-        "FN",
-        "ALG"
-      ],
-      "post_filter": "ts_weak_hash_algorithm",
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-weak-hash.yml"
-    },
-    {
-      "id": "ts-xss-dom-sink",
-      "name": "XSS DOM Sink",
-      "severity": "error",
-      "language": "typescript",
-      "message": "XSS risk — dynamic value written to innerHTML/outerHTML or document.write()",
-      "query": "  [\n    (assignment_expression\n      left: (member_expression\n        property: (property_identifier) @PROP)\n      right: (identifier) @VALUE\n      (#match? @PROP \"^(innerHTML|outerHTML)$\"))\n    (assignment_expression\n      left: (member_expression\n        property: (property_identifier) @PROP)\n      right: (member_expression) @VALUE\n      (#match? @PROP \"^(innerHTML|outerHTML)$\"))\n    (assignment_expression\n      left: (member_expression\n        property: (property_identifier) @PROP)\n      right: (call_expression) @VALUE\n      (#match? @PROP \"^(innerHTML|outerHTML)$\"))\n    (assignment_expression\n      left: (member_expression\n        property: (property_identifier) @PROP)\n      right: (await_expression) @VALUE\n      (#match? @PROP \"^(innerHTML|outerHTML)$\"))\n  ]\n  [\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (identifier) @ARG)\n      (#eq? @OBJ \"document\")\n      (#match? @FN \"^(write|writeln)$\"))\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (member_expression) @ARG)\n      (#eq? @OBJ \"document\")\n      (#match? @FN \"^(write|writeln)$\"))\n    (call_expression\n      function: (member_expression\n        object: (identifier) @OBJ\n        property: (property_identifier) @FN)\n      arguments: (arguments (call_expression) @ARG)\n      (#eq? @OBJ \"document\")\n      (#match? @FN \"^(write|writeln)$\"))\n  ]",
-      "metavars": [
-        "PROP",
-        "VALUE",
-        "OBJ",
-        "FN",
-        "ARG"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/ts-xss-dom-sink.yml"
-    },
-    {
-      "id": "unsafe-regex",
-      "name": "Dynamic Regex Construction",
-      "severity": "error",
-      "language": "typescript",
-      "message": "Dynamic regex from user input — can cause ReDoS (Regular Expression Denial of Service)",
-      "query": "  (new_expression\n    constructor: (identifier) @CTOR\n    (#eq? @CTOR \"RegExp\")\n    arguments: (arguments\n      (template_string\n        (template_substitution) @INTERPOLATION) @PATTERN)\n    (#not-match? @INTERPOLATION \"escape|Escape|replace\"))",
-      "metavars": [
-        "CTOR",
-        "INTERPOLATION",
-        "PATTERN"
-      ],
-      "defect_class": "injection",
-      "inline_tier": "blocking",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/unsafe-regex.yml"
-    },
-    {
-      "id": "variable-shadowing",
-      "name": "Variable Shadowing",
-      "severity": "warning",
-      "language": "typescript",
-      "message": "Variable '{{NAME}}' shadows a parameter — use a distinct name",
-      "query": "  (function_declaration\n    parameters: (formal_parameters\n      (required_parameter\n        pattern: (identifier) @PARAM))\n    body: (statement_block\n      (lexical_declaration\n        (variable_declarator\n          name: (identifier) @NAME))))",
-      "metavars": [
-        "PARAM",
-        "NAME"
-      ],
-      "post_filter": "name_matches_param",
-      "defect_class": "safety",
-      "inline_tier": "review",
-      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/typescript/variable-shadowing.yml"
-    }
-  ]
-}

apps/web/src/api/config_profiles.ts

@@ -1,189 +0,0 @@
-import { apiClient } from "./client";
-
-export interface ConfigProfile {
-	id: string;
-	user_id: string;
-	name: string;
-	description: string | null;
-	project_id: string | null;
-	tool_type_id: string | null;
-	env_vars: Record<string, string>;
-	runtime_hints: Record<string, unknown>;
-	mounts: ConfigProfileMount[];
-	git_mounts: GitMount[];
-	files: Record<string, string>;
-	is_default: boolean;
-	includes: ConfigProfileInclude[];
-	created_at: string;
-	updated_at: string;
-}
-
-export interface ConfigProfileMount {
-	target: string;
-	mode: "ro" | "rw";
-	files: Record<string, string>;
-}
-
-export interface GitMountMapping {
-	source_path: string;
-	target_path: string;
-}
-
-export interface GitMount {
-	remote_url: string;
-	branch?: string;
-	mappings: GitMountMapping[];
-	// Legacy fields (for backward compatibility when reading old data)
-	source_path?: string;
-	target_path?: string;
-}
-
-export interface ConfigProfileInclude {
-	id: string;
-	included_profile_id: string;
-	order_index: number;
-}
-
-export interface ResolvedProfile {
-	profile_id: string;
-	profile_name: string;
-	env_vars: Record<string, string>;
-	runtime_hints: Record<string, unknown>;
-	mounts: ResolvedMount[];
-	git_mounts: GitMount[];
-	files: Record<string, string>;
-	overrides: {
-		env_vars: Record<string, string>;
-		runtime_hints: Record<string, string>;
-		files: Record<string, string>;
-		mounts: Record<string, string>;
-	};
-	included_profiles: Array<{ id: string; name: string }>;
-}
-
-export interface ResolvedMount {
-	target: string;
-	mode: "ro" | "rw";
-	files: Record<string, string>;
-	overridden_files: Record<string, string>;
-}
-
-export interface CreateConfigProfileRequest {
-	name: string;
-	description?: string;
-	project_id?: string;
-	tool_type_id?: string;
-	env_vars?: Record<string, string>;
-	runtime_hints?: Record<string, unknown>;
-	mounts?: ConfigProfileMount[];
-	git_mounts?: GitMount[];
-	files?: Record<string, string>;
-	is_default?: boolean;
-}
-
-export interface UpdateConfigProfileRequest {
-	name?: string;
-	description?: string;
-	project_id?: string;
-	tool_type_id?: string;
-	env_vars?: Record<string, string>;
-	runtime_hints?: Record<string, unknown>;
-	mounts?: ConfigProfileMount[];
-	git_mounts?: GitMount[];
-	files?: Record<string, string>;
-	is_default?: boolean;
-}
-
-export interface UpdateIncludesRequest {
-	includes: string[];
-}
-
-export const listConfigProfiles = async (
-	projectId?: string,
-	toolTypeId?: string,
-): Promise<ConfigProfile[]> => {
-	const response = await apiClient.get<ConfigProfile[]>("/config-profiles", {
-		params: { project_id: projectId, tool_type_id: toolTypeId },
-	});
-	return response.data;
-};
-
-export const getConfigProfile = async (id: string): Promise<ConfigProfile> => {
-	const response = await apiClient.get<ConfigProfile>(`/config-profiles/${id}`);
-	return response.data;
-};
-
-export const createConfigProfile = async (
-	data: CreateConfigProfileRequest,
-): Promise<ConfigProfile> => {
-	const response = await apiClient.post<ConfigProfile>(
-		"/config-profiles",
-		data,
-	);
-	return response.data;
-};
-
-export const updateConfigProfile = async (
-	id: string,
-	data: UpdateConfigProfileRequest,
-): Promise<ConfigProfile> => {
-	const response = await apiClient.put<ConfigProfile>(
-		`/config-profiles/${id}`,
-		data,
-	);
-	return response.data;
-};
-
-export const deleteConfigProfile = async (id: string): Promise<void> => {
-	await apiClient.delete(`/config-profiles/${id}`);
-};
-
-export const updateProfileIncludes = async (
-	id: string,
-	data: UpdateIncludesRequest,
-): Promise<ConfigProfile> => {
-	const response = await apiClient.put<ConfigProfile>(
-		`/config-profiles/${id}/includes`,
-		data,
-	);
-	return response.data;
-};
-
-export const previewConfigProfile = async (
-	id: string,
-): Promise<ResolvedProfile> => {
-	const response = await apiClient.get<ResolvedProfile>(
-		`/config-profiles/${id}/preview`,
-	);
-	return response.data;
-};
-
-export const resolveDefaultProfile = async (
-	projectId: string,
-	toolTypeId: string,
-): Promise<{ profile_id: string | null; profile_name: string | null }> => {
-	const response = await apiClient.get("/config-profiles/defaults/resolve", {
-		params: { project_id: projectId, tool_type_id: toolTypeId },
-	});
-	return response.data;
-};
-
-export interface ValidateGitUrlResponse {
-	valid: boolean;
-	suggested_url?: string;
-	branches?: string[];
-	default_branch?: string;
-	error?: string;
-	error_code?: string;
-}
-
-export const validateGitUrl = async (
-	url: string,
-	sshKeyId?: string,
-): Promise<ValidateGitUrlResponse> => {
-	const response = await apiClient.post<ValidateGitUrlResponse>(
-		"/config-profiles/validate-git-url",
-		{ url, ssh_key_id: sshKeyId },
-	);
-	return response.data;
-};

apps/web/src/api/events.ts

@@ -1,22 +0,0 @@
-const BASE_URL = import.meta.env.VITE_API_BASE_URL ?? "http://localhost:8000";
-
-export function createEventSource(): EventSource {
-	return new EventSource(`${BASE_URL}/events/stream`, {
-		withCredentials: true,
-	});
-}
-
-export async function probeEventStreamStatus(): Promise<number | null> {
-	try {
-		const controller = new AbortController();
-		const timer = setTimeout(() => controller.abort(), 2000);
-		const res = await fetch(`${BASE_URL}/events/stream`, {
-			credentials: "include",
-			signal: controller.signal,
-		});
-		clearTimeout(timer);
-		return res.status;
-	} catch {
-		return null;
-	}
-}

apps/web/src/api/git_repositories.ts

@@ -1,299 +0,0 @@
-import { apiClient } from "./client";
-
-export interface GitRepository {
-  id: string;
-  name: string;
-  path: string;
-  project_id: string;
-  owner_id: string;
-  is_mirror: boolean;
-  remote_url: string | null;
-  ssh_key_id: string | null;
-  last_push: string | null;
-  created_at: string | null;
-}
-
-export interface GitRepositoryCreate {
-  name: string;
-  remote_url?: string;
-  force_original_url?: boolean;
-  ssh_key_id?: string;
-}
-
-export interface URLParseResult {
-  original_url: string;
-  base_url: string | null;
-  is_valid_clone_url: boolean;
-  needs_parsing: boolean;
-  host: string | null;
-  message: string;
-  error_code: string | null;
-}
-
-export async function parseGitUrl(url: string): Promise<URLParseResult> {
-  const response = await apiClient.post("/repositories/parse-url", { url });
-  return response.data;
-}
-
-export async function listRepositories(projectId?: string): Promise<GitRepository[]> {
-  if (projectId) {
-    const response = await apiClient.get<GitRepository[]>(
-      `/projects/${projectId}/repositories`
-    );
-    return response.data;
-  }
-  // List all user repositories (including external)
-  const response = await apiClient.get<GitRepository[]>("/repositories");
-  return response.data;
-}
-
-export async function listAllUserRepositories(): Promise<GitRepository[]> {
-  const response = await apiClient.get<GitRepository[]>("/repositories");
-  return response.data;
-}
-
-export async function createRepository(
-  projectId: string,
-  data: GitRepositoryCreate
-): Promise<GitRepository> {
-  const response = await apiClient.post(`/projects/${projectId}/repositories`, data);
-  return response.data;
-}
-
-export async function createExternalRepository(
-  data: GitRepositoryCreate
-): Promise<GitRepository> {
-  const response = await apiClient.post<GitRepository>("/repositories", data);
-  return response.data;
-}
-
-export async function deleteRepository(projectId: string, repoId: string): Promise<void> {
-  await apiClient.delete(`/projects/${projectId}/repositories/${repoId}`);
-}
-
-export async function updateRepositorySshKey(
-  projectId: string,
-  repoId: string,
-  sshKeyId: string | null
-): Promise<GitRepository> {
-  const response = await apiClient.patch(
-    `/projects/${projectId}/repositories/${repoId}/ssh-key`,
-    { ssh_key_id: sshKeyId }
-  );
-  return response.data;
-}
-
-export interface Branch {
-  name: string;
-  is_default: boolean;
-  last_commit: string | null;
-}
-
-export interface BranchesResponse {
-  branches: Branch[];
-  default_branch: string;
-}
-
-export async function listRepositoryBranches(
-  projectId: string,
-  repoId: string
-): Promise<BranchesResponse> {
-  const response = await apiClient.get(
-    `/projects/${projectId}/repositories/${repoId}/branches`
-  );
-  return response.data;
-}
-
-export interface CommitHistoryEntry {
-  hash: string;
-  short_hash: string;
-  message: string;
-  author_name: string;
-  author_email: string;
-  author_date: string;
-  refs: string[];
-  graph_symbol: string;
-  graph_depth: number;
-}
-
-export interface CommitHistoryResponse {
-  commits: CommitHistoryEntry[];
-  branches: string[];
-  tags: string[];
-}
-
-export async function getRepositoryHistory(
-  projectId: string,
-  repoId: string,
-  branch?: string,
-  limit?: number
-): Promise<CommitHistoryResponse> {
-  const searchParams = new URLSearchParams();
-  if (branch) searchParams.set("branch", branch);
-  if (limit) searchParams.set("limit", String(limit));
-  const queryString = searchParams.toString();
-  const params = queryString ? `?${queryString}` : "";
-  const response = await apiClient.get(`/projects/${projectId}/repositories/${repoId}/history${params}`);
-  return response.data;
-}
-
-export interface CommitDetail {
-  hash: string;
-  short_hash: string;
-  message: string;
-  author_name: string;
-  author_email: string;
-  author_date: string;
-  committer_name: string;
-  committer_email: string;
-  committer_date: string;
-  stats: {
-    additions: number;
-    deletions: number;
-    files_changed: number;
-  };
-  diff: string;
-  parents: string[];
-}
-
-export async function getCommitDetail(
-  projectId: string,
-  repoId: string,
-  commitHash: string
-): Promise<CommitDetail> {
-  const response = await apiClient.get(
-    `/projects/${projectId}/repositories/${repoId}/commits/${commitHash}`
-  );
-  return response.data;
-}
-
-// Git Control API
-
-export interface GitStatus {
-  branch: string;
-  modified: string[];
-  added: string[];
-  deleted: string[];
-  untracked: string[];
-  renamed: string[];
-  ahead: number;
-  behind: number;
-}
-
-export async function getRepositoryStatus(
-  projectId: string,
-  repoId: string
-): Promise<GitStatus> {
-  const response = await apiClient.get(
-    `/projects/${projectId}/repositories/${repoId}/status`
-  );
-  return response.data;
-}
-
-export async function createBranch(
-  projectId: string,
-  repoId: string,
-  name: string,
-  baseBranch: string = "HEAD"
-): Promise<{ message: string; branch: string }> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/branches`,
-    { name, base_branch: baseBranch }
-  );
-  return response.data;
-}
-
-export async function deleteBranch(
-  projectId: string,
-  repoId: string,
-  branchName: string,
-  force: boolean = false
-): Promise<{ message: string }> {
-  const response = await apiClient.delete(
-    `/projects/${projectId}/repositories/${repoId}/branches/${branchName}?force=${force}`
-  );
-  return response.data;
-}
-
-export async function checkoutBranch(
-  projectId: string,
-  repoId: string,
-  branch: string
-): Promise<{ message: string; branch: string }> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/checkout`,
-    { branch }
-  );
-  return response.data;
-}
-
-export interface CommitResponse {
-  commit_hash: string;
-  message: string;
-}
-
-export async function commitChanges(
-  projectId: string,
-  repoId: string,
-  message: string,
-  files?: string[]
-): Promise<CommitResponse> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/commit`,
-    { message, files }
-  );
-  return response.data;
-}
-
-export async function fetchRepository(
-  projectId: string,
-  repoId: string
-): Promise<{ message: string }> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/fetch`
-  );
-  return response.data;
-}
-
-export async function pullRepository(
-  projectId: string,
-  repoId: string,
-  branch?: string
-): Promise<{ message: string }> {
-  const params = branch ? `?branch=${branch}` : "";
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/pull${params}`
-  );
-  return response.data;
-}
-
-export async function pushRepository(
-  projectId: string,
-  repoId: string,
-  branch?: string
-): Promise<{ message: string }> {
-  const params = branch ? `?branch=${branch}` : "";
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/push${params}`
-  );
-  return response.data;
-}
-
-export interface MergeResponse {
-  commit_hash: string;
-  message: string;
-}
-
-export async function mergeBranches(
-  projectId: string,
-  repoId: string,
-  sourceBranch: string,
-  targetBranch?: string,
-  message?: string
-): Promise<MergeResponse> {
-  const response = await apiClient.post(
-    `/projects/${projectId}/repositories/${repoId}/merge`,
-    { source_branch: sourceBranch, target_branch: targetBranch, message }
-  );
-  return response.data;
-}

apps/web/src/api/notifications.ts

@@ -1,73 +0,0 @@
-import { apiClient } from "./client";
-
-export interface NotificationItem {
-	id: string;
-	user_id: string;
-	category: string;
-	severity: "info" | "warning" | "error" | "success";
-	title: string;
-	message: string | null;
-	source_type: string | null;
-	source_id: string | null;
-	metadata: Record<string, unknown>;
-	read_at: string | null;
-	dismissed_at: string | null;
-	created_at: string;
-}
-
-export interface NotificationListResponse {
-	items: NotificationItem[];
-	total: number;
-	limit: number;
-	offset: number;
-}
-
-export interface UnreadCountResponse {
-	count: number;
-}
-
-export interface MarkAllReadResponse {
-	marked_count: number;
-}
-
-export interface ClearAllResponse {
-	cleared_count: number;
-}
-
-export const getNotifications = async (): Promise<NotificationListResponse> => {
-	const response =
-		await apiClient.get<NotificationListResponse>("/notifications");
-	return response.data;
-};
-
-export const getUnreadCount = async (): Promise<number> => {
-	const response = await apiClient.get<UnreadCountResponse>(
-		"/notifications/unread",
-	);
-	return response.data.count;
-};
-
-export const markNotificationRead = async (
-	id: string,
-): Promise<NotificationItem> => {
-	const response = await apiClient.patch<NotificationItem>(
-		`/notifications/${id}/read`,
-	);
-	return response.data;
-};
-
-export const markAllNotificationsRead = async (): Promise<number> => {
-	const response = await apiClient.post<MarkAllReadResponse>(
-		"/notifications/mark-all-read",
-	);
-	return response.data.marked_count;
-};
-
-export const dismissNotification = async (id: string): Promise<void> => {
-	await apiClient.delete(`/notifications/${id}`);
-};
-
-export const clearAllNotifications = async (): Promise<number> => {
-	const response = await apiClient.delete<ClearAllResponse>("/notifications");
-	return response.data.cleared_count;
-};

apps/web/src/api/ssh_keys.ts

@@ -1,53 +0,0 @@
-import { apiClient } from "./client";
-
-export interface SSHKey {
-  id: string;
-  name: string;
-  public_key: string;
-  created_at: string;
-}
-
-export interface SSHKeyCreate {
-  name: string;
-}
-
-export async function listSSHKeys(): Promise<SSHKey[]> {
-  const response = await apiClient.get<SSHKey[]>("/ssh-keys");
-  return response.data;
-}
-
-export async function createSSHKey(data: SSHKeyCreate): Promise<SSHKey> {
-  const response = await apiClient.post<SSHKey>("/ssh-keys", data);
-  return response.data;
-}
-
-export async function deleteSSHKey(keyId: string): Promise<void> {
-  await apiClient.delete(`/ssh-keys/${keyId}`);
-}
-
-export interface SignPayloadRequest {
-  payload: string;
-}
-
-export interface SignatureResponse {
-  signature: string;
-}
-
-export interface VerifySignatureRequest {
-  payload: string;
-  signature: string;
-}
-
-export interface VerifySignatureResponse {
-  valid: boolean;
-}
-
-export async function signPayload(keyId: string, data: SignPayloadRequest): Promise<SignatureResponse> {
-  const response = await apiClient.post<SignatureResponse>(`/ssh-keys/${keyId}/sign`, data);
-  return response.data;
-}
-
-export async function verifySignature(keyId: string, data: VerifySignatureRequest): Promise<VerifySignatureResponse> {
-  const response = await apiClient.post<VerifySignatureResponse>(`/ssh-keys/${keyId}/verify`, data);
-  return response.data;
-}