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": "fdea8a74bb4c7449c01c4bd61646c895b10ede78"
-}

.atl/skill-registry.md

@@ -1,36 +0,0 @@
-# Skill Registry — headquarter
-
-<!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
-
-Last updated: 2026-05-28
-
-## 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` | Use OpenSpec as the source of truth for planning, implementation, verification, and archive discipline. | user | `/home/alex/.config/opencode/skills/openspec/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

.gitignore

@@ -48,9 +48,8 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
-/.stoneforge/.worktrees/
+
-# Pi / agent cache
+# Local runtime state
-.pi/
 .atl/
-.sisyphus/
+.pi/
-.pi-lens/
+swap-pane

.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-5fe","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:40.892Z","createdBy":"el-2jua"}
-{"blockedId":"el-1nj","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.010Z","createdBy":"el-2jua"}
-{"blockedId":"el-1bn","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.127Z","createdBy":"el-2jua"}
-{"blockedId":"el-4hr","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.244Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.372Z","createdBy":"el-2jua"}
-{"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"}
-{"blockedId":"el-2xl","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.844Z","createdBy":"el-2jua"}
-{"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"}
-{"blockedId":"el-4hr","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.868Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:42.979Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.092Z","createdBy":"el-2jua"}
-{"blockedId":"el-5z8","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.205Z","createdBy":"el-2jua"}
-{"blockedId":"el-5z8","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.313Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.422Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.529Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:43.647Z","createdBy":"el-2jua"}
-{"blockedId":"el-5j5","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.758Z","createdBy":"el-2jua"}
-{"blockedId":"el-2xl","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.876Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.987Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:44.096Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:44.208Z","createdBy":"el-2jua"}
-{"blockedId":"el-107","blockerId":"el-5z8","type":"blocks","createdAt":"2026-05-24T12:44:44.319Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-5j5","type":"blocks","createdAt":"2026-05-24T12:44:44.429Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-2xl","type":"blocks","createdAt":"2026-05-24T12:44:44.539Z","createdBy":"el-2jua"}
-{"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"}
-{"blockedId":"el-14w","blockerId":"el-32e","type":"blocks","createdAt":"2026-05-24T12:44:44.873Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-3ou","type":"blocks","createdAt":"2026-05-24T12:44:44.987Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-14w","type":"blocks","createdAt":"2026-05-24T12:44:45.107Z","createdBy":"el-2jua"}
-{"blockedId":"el-375","blockerId":"el-26p","type":"replies-to","createdAt":"2026-05-24T13:21:42.486Z","createdBy":"el-2i1s"}
-{"blockedId":"el-3n4","blockerId":"el-31p","type":"replies-to","createdAt":"2026-05-24T13:21:46.044Z","createdBy":"el-13ju"}
-{"blockedId":"el-3jer","blockerId":"el-1xx","type":"replies-to","createdAt":"2026-05-24T13:24:47.580Z","createdBy":"el-4350"}
-{"blockedId":"el-1afv","blockerId":"el-1ozw","type":"replies-to","createdAt":"2026-05-24T13:32:42.658Z","createdBy":"el-51a8"}

AGENTS.md

@@ -4,10 +4,6 @@
 
 OpenSpec is the source of truth. Superpowers is the default workflow. Keep changes small, scoped, and verified.
 
-## Communication
-
-All agent output, code comments, commit messages, documentation, and artifacts must be in **English** unless the user explicitly requests another language.
-
 ## Priority order
 
 1. Current user instruction
@@ -91,31 +87,6 @@ Do not claim completion without verification evidence.
 
 ## Git workflow
 
-### Branching strategy
-
-For every spec change or new functionality:
-
-1. Create a new branch from `dev` with a proper prefix:
-   - `feat/` for new features (e.g., `feat/tool-workshop`)
-   - `fix/` for bug fixes (e.g., `fix/terminal-tty`)
-   - `refactor/` for refactors (e.g., `refactor/api-cleanup`)
-   - `docs/` for documentation (e.g., `docs/api-guide`)
-   - `chore/` for maintenance (e.g., `chore/update-deps`)
-2. Branch name should reference the OpenSpec change name when applicable.
-3. Do not commit directly to `main` or `dev`.
-
-### Completion and merge
-
-When implementation is complete and verified:
-
-1. Ensure all tests pass and quality gates are met.
-2. Stage all changes with `git add -A`.
-3. Create a commit with a proper conventional commit message (see below).
-4. Switch to `dev`: `git checkout dev`.
-5. Merge the feature branch: `git merge --no-ff <branch-name>`.
-6. Push to remote: `git push origin dev`.
-7. Delete the local feature branch if desired: `git branch -d <branch-name>`.
-
 ### Auto-commit on spec completion
 
 When an OpenSpec change is fully implemented and all tasks are complete:

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **User Settings** - Theme selection, git identity, and preference management
 - **SSH Key Management** - Ed25519 key generation with secure storage
 - **Tool Types** - Built-in development tools (code-server, jupyter-notebook) with custom type support
+- **Config Profiles** - User-owned profile CRUD with includes, mounts, path validation, cycle detection, and default profile selection
 - **Comprehensive Documentation** - Architecture, API, deployment, and development guides
 
 ### Changed

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/Dockerfile

@@ -27,7 +27,6 @@ WORKDIR /app
 RUN apt-get update && apt-get install -y --no-install-recommends \
     libpq5 \
     git \
-    openssh-client \
     netcat-openbsd \
     ca-certificates \
     curl \

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

@@ -0,0 +1,104 @@
+"""add config profiles, includes, mounts, and tool instance profile selection
+
+Revision ID: 0013_add_config_profiles
+Revises: 0012_default_port_req
+Create Date: 2026-05-24 12:00:00.000000
+
+"""
+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 = "0013_add_config_profiles"
+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:
+    # Create config_profiles table
+    op.create_table(
+        "config_profiles",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("name", sa.String(length=255), nullable=False),
+        sa.Column("description", sa.Text(), 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.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
+    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+
+    # Create config_includes table
+    op.create_table(
+        "config_includes",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), 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.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["included_profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
+    )
+    op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    op.create_index("idx_config_includes_included", "config_includes", ["included_profile_id"])
+
+    # Create config_mounts table
+    op.create_table(
+        "config_mounts",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("mount_path", sa.String(length=1024), nullable=False),
+        sa.Column("content", sa.Text(), nullable=True),
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        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.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+
+    # Add selected_profile_id to tool_instances
+    op.add_column(
+        "tool_instances",
+        sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.create_foreign_key(
+        "fk_tool_instances_selected_profile",
+        "tool_instances",
+        "config_profiles",
+        ["selected_profile_id"],
+        ["id"],
+        ondelete="SET NULL",
+    )
+    op.create_index("idx_tool_instances_selected_profile", "tool_instances", ["selected_profile_id"])
+
+
+def downgrade() -> None:
+    # Remove selected_profile_id from tool_instances
+    op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
+    op.drop_constraint("fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey")
+    op.drop_column("tool_instances", "selected_profile_id")
+
+    # Drop config_mounts
+    op.drop_index("idx_config_mounts_profile", table_name="config_mounts")
+    op.drop_table("config_mounts")
+
+    # Drop config_includes
+    op.drop_index("idx_config_includes_included", table_name="config_includes")
+    op.drop_index("idx_config_includes_profile", table_name="config_includes")
+    op.drop_table("config_includes")
+
+    # Drop config_profiles
+    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
+    op.drop_table("config_profiles")

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_add_profile_resolver_fields.py

@@ -0,0 +1,119 @@
+"""add profile resolver fields to config profiles and mounts
+
+Revision ID: 0014_add_profile_resolver_fields
+Revises: 0013_add_config_profiles
+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 = "0014_add_profile_resolver_fields"
+down_revision: Union[str, None] = "0013_add_config_profiles"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Add fields to config_profiles
+    op.add_column(
+        "config_profiles",
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("environment_variables", sa.JSON(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("start_command", sa.Text(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("working_directory", sa.Text(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("port", sa.Integer(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+    )
+    
+    # Add foreign keys for project and tool_type
+    op.create_foreign_key(
+        "fk_config_profiles_project",
+        "config_profiles",
+        "projects",
+        ["project_id"],
+        ["id"],
+        ondelete="CASCADE",
+    )
+    op.create_foreign_key(
+        "fk_config_profiles_tool_type",
+        "config_profiles",
+        "tool_types",
+        ["tool_type_id"],
+        ["id"],
+        ondelete="CASCADE",
+    )
+    
+    # Create indices
+    op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    op.create_index("idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"])
+    
+    # Alter config_mounts: rename mount_path to target_path, add mode, change content to files JSON
+    op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
+    op.add_column(
+        "config_mounts",
+        sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
+    )
+    op.add_column(
+        "config_mounts",
+        sa.Column("files", sa.JSON(), nullable=True),
+    )
+    # Drop the source_profile foreign key if it exists
+    op.drop_constraint(
+        "config_mounts_source_profile_id_fkey",
+        "config_mounts",
+        type_="foreignkey",
+    )
+    op.drop_column("config_mounts", "content")
+    op.drop_column("config_mounts", "source_profile_id")
+
+
+def downgrade() -> None:
+    # Restore config_mounts
+    op.add_column(
+        "config_mounts",
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_mounts",
+        sa.Column("content", sa.Text(), nullable=True),
+    )
+    op.drop_column("config_mounts", "files")
+    op.drop_column("config_mounts", "mode")
+    op.alter_column("config_mounts", "target_path", new_column_name="mount_path")
+    
+    # Restore config_profiles
+    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_constraint("fk_config_profiles_tool_type", "config_profiles", type_="foreignkey")
+    op.drop_constraint("fk_config_profiles_project", "config_profiles", type_="foreignkey")
+    op.drop_column("config_profiles", "is_default")
+    op.drop_column("config_profiles", "port")
+    op.drop_column("config_profiles", "working_directory")
+    op.drop_column("config_profiles", "start_command")
+    op.drop_column("config_profiles", "environment_variables")
+    op.drop_column("config_profiles", "tool_type_id")
+    op.drop_column("config_profiles", "project_id")

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/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/__init__.py

@@ -1,6 +1,4 @@
 from src.api.auth import router as auth_router
-from src.api.events import router as events_router
-from src.api.notifications import router as notifications_router
 from src.api.users import router as users_router
 
-__all__ = ["auth_router", "events_router", "notifications_router", "users_router"]
+__all__ = ["auth_router", "users_router"]

apps/api/src/api/auth.py

@@ -48,7 +48,7 @@ async def login(next: str = "/") -> RedirectResponse:
         redirect_uri=redirect_uri,
         state=state,
     )
-    logger.debug("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
+    logger.info("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
     response = RedirectResponse(location)
     response.set_cookie("auth_state", state, httponly=True, samesite="lax")
     response.set_cookie("auth_next", next, httponly=True, samesite="lax")
@@ -63,7 +63,7 @@ async def callback(
     auth_next: str | None = Cookie(default="/"),
     session: AsyncSession = Depends(get_db_session),
 ) -> RedirectResponse:
-    logger.debug("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
+    logger.info("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
     
     if auth_state is None or auth_state != state:
         logger.warning("State mismatch: cookie=%s, param=%s", auth_state, state)
@@ -71,7 +71,7 @@ async def callback(
 
     settings = Settings()
     redirect_uri = f"{settings.api_base_url}/auth/callback"
-    logger.debug("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
+    logger.info("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
     
     async with httpx.AsyncClient() as client:
         try:
@@ -92,7 +92,7 @@ async def callback(
                 access_token=token_payload["access_token"],
                 client=client,
             )
-            logger.debug("User info fetched successfully")
+            logger.info("User info fetched successfully")
         except Exception as exc:
             logger.error("User info fetch failed: %s", exc)
             raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="failed to fetch user info")
@@ -100,19 +100,19 @@ async def callback(
     authentik_id = str(user_info.get("sub", ""))
     email = str(user_info.get("email", f"{authentik_id}@authentik.local"))
     name = str(user_info.get("name", email))
-    logger.debug("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
+    logger.info("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
 
     try:
         user = await session.scalar(select(User).where(User.authentik_id == authentik_id))
         if user is None:
-            logger.debug("Creating new user: authentik_id=%s", authentik_id)
+            logger.info("Creating new user: authentik_id=%s", authentik_id)
             user = User(email=email, name=name, authentik_id=authentik_id, avatar_url=None)
             session.add(user)
             await session.commit()
             await session.refresh(user)
             logger.info("New user created: id=%s", user.id)
         else:
-            logger.debug("Existing user found: id=%s, updating info", user.id)
+            logger.info("Existing user found: id=%s, updating info", user.id)
             user.email = email
             user.name = name
             await session.commit()
@@ -165,20 +165,20 @@ async def me(
     session_cookie: str | None = Cookie(default=None, alias="session"),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict[str, Any]:
-    logger.debug("Auth /me called, cookie present: %s", bool(session_cookie))
+    logger.info("Auth /me called, cookie present: %s", bool(session_cookie))
     
     if not session_cookie:
         logger.warning("Auth /me: missing session cookie")
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")
 
     settings = Settings()
-    logger.debug("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
+    logger.info("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
                 settings.cookie_domain, settings.cookie_secure, settings.cookie_samesite)
     
     try:
         payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
         user_id = payload["user_id"]
-        logger.debug("Auth /me: decoded session for user_id=%s", user_id)
+        logger.info("Auth /me: decoded session for user_id=%s", user_id)
     except ValueError as exc:
         logger.warning("Auth /me: invalid session: %s", exc)
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc))

apps/api/src/api/config_folders.py

@@ -0,0 +1,284 @@
+"""Config folder API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import 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.config_folder import ConfigFolder
+from src.schemas.config_folder import (
+    ConfigFolderCreate,
+    ConfigFolderUpdate,
+    ConfigFolderResponse,
+    ProjectOverrideCreate,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-folders", tags=["config-folders"])
+
+
+@router.get("", summary="List config folders", description="Get all config folders for the current user.")
+async def list_config_folders(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """List config folders for the current user."""
+    query = select(ConfigFolder).where(ConfigFolder.user_id == user_id)
+    result = await session.execute(query)
+    folders = result.scalars().all()
+    
+    return {
+        "folders": [
+            {
+                "id": str(f.id),
+                "user_id": str(f.user_id),
+                "name": f.name,
+                "description": f.description,
+                "mount_path": f.mount_path,
+                "files": f.files,
+                "project_overrides": f.project_overrides,
+                "is_active": f.is_active,
+                "created_at": f.created_at.isoformat() if f.created_at else None,
+                "updated_at": f.updated_at.isoformat() if f.updated_at else None,
+            }
+            for f in folders
+        ]
+    }
+
+
+@router.post("", summary="Create config folder", description="Create a new config folder.", status_code=status.HTTP_201_CREATED)
+async def create_config_folder(
+    data: ConfigFolderCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a config folder."""
+    # Check for duplicate name
+    existing = await session.scalar(
+        select(ConfigFolder).where(
+            ConfigFolder.user_id == user_id,
+            ConfigFolder.name == data.name,
+        )
+    )
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config folder with name '{data.name}' already exists"
+        )
+    
+    folder = ConfigFolder(
+        user_id=user_id,
+        name=data.name,
+        description=data.description,
+        mount_path=data.mount_path,
+        files=data.files,
+    )
+    session.add(folder)
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.put("/{folder_id}", summary="Update config folder", description="Update an existing config folder.")
+async def update_config_folder(
+    folder_id: uuid.UUID,
+    data: ConfigFolderUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    if data.name is not None:
+        folder.name = data.name
+    if data.description is not None:
+        folder.description = data.description
+    if data.mount_path is not None:
+        folder.mount_path = data.mount_path
+    if data.files is not None:
+        folder.files = data.files
+    if data.is_active is not None:
+        folder.is_active = data.is_active
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.delete("/{folder_id}", summary="Delete config folder", description="Delete a config folder.", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    await session.delete(folder)
+    await session.commit()
+
+
+class ProjectOverrideWithId(ProjectOverrideCreate):
+    project_id: uuid.UUID = Field(description="Project ID for the override")
+
+
+@router.get("/{folder_id}", summary="Get config folder by ID", description="Get a single config folder by its ID.")
+async def get_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get a config folder by ID."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.post("/{folder_id}/overrides", summary="Add project override", description="Add a project override to a config folder.")
+async def add_project_override(
+    folder_id: uuid.UUID,
+    data: ProjectOverrideWithId,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Add a project override to a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Add/update override
+    override_data = {}
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    # Use a copy to trigger SQLAlchemy change detection on JSONB
+    current_overrides = dict(folder.project_overrides or {})
+    current_overrides[str(data.project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.put("/{folder_id}/overrides/{project_id}", summary="Update project override", description="Update a project override.")
+async def update_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    data: ProjectOverrideCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Update override
+    current_overrides = dict(folder.project_overrides or {})
+    override_data = current_overrides.get(str(project_id), {})
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    current_overrides[str(project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    # Mark the field as modified to ensure SQLAlchemy detects the change
+    from sqlalchemy.orm.attributes import flag_modified
+    flag_modified(folder, "project_overrides")
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.delete("/{folder_id}/overrides/{project_id}", summary="Remove project override", description="Remove a project override.")
+async def remove_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Remove a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Remove override if exists
+    current_overrides = dict(folder.project_overrides or {})
+    if str(project_id) in current_overrides:
+        del current_overrides[str(project_id)]
+        folder.project_overrides = current_overrides
+        await session.commit()
+        await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides or {},
+    }

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 = 5
-
-
-@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/health.py

@@ -4,11 +4,18 @@ import time
 from datetime import datetime, timezone
 from typing import Any
 
-from fastapi import APIRouter
+from fastapi import APIRouter, status
-from pydantic import BaseModel, Field
 from sqlalchemy import text
 
+from src.config import Settings
 from src.database import SessionLocal
+from src.schemas.health import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
 
 router = APIRouter()
 
@@ -16,45 +23,6 @@ router = APIRouter()
 _start_time = time.time()
 
 
-class DatabaseHealth(BaseModel):
-    """Database health check result."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
-class DiskHealth(BaseModel):
-    """Disk space health check result."""
-
-    status: str = Field(description="Disk health status", examples=["healthy"])
-    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
-    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
-
-
-class HealthChecks(BaseModel):
-    """Individual health checks."""
-
-    database: DatabaseHealth | None = None
-    disk: DiskHealth | None = None
-
-
-class HealthResponse(BaseModel):
-    """Overall health check response."""
-
-    status: str = Field(description="Overall health status", examples=["healthy"])
-    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
-    version: str = Field(description="API version", examples=["0.1.0"])
-    checks: HealthChecks = Field(description="Individual health checks")
-    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
-
-
-class DatabaseHealthResponse(BaseModel):
-    """Database-specific health check response."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
 @router.get(
     "/health",
     response_model=HealthResponse,

apps/api/src/api/instance_proxy.py

@@ -2,6 +2,7 @@
 
 import logging
 import uuid
+from typing import Any
 
 import httpx
 from fastapi import APIRouter, Depends, HTTPException, Request, Response, status

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/projects.py

@@ -3,41 +3,24 @@ import shutil
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
 from src.models.git_repository import GitRepository
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
+from src.models.user import User
+from src.schemas.project import (
+    ProjectCreate,
+    ProjectUpdate,
+    ProjectResponse,
+    SetDefaultSSHKeyRequest,
+)
 
 router = APIRouter(prefix="/projects", tags=["projects"])
 
 
-class ProjectCreate(BaseModel):
-    name: str
-    description: str | None = None
-
-
-class ProjectUpdate(BaseModel):
-    name: str | None = None
-    description: str | None = None
-
-
-class ProjectResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    description: str | None
-    owner_id: uuid.UUID
-    default_ssh_key_id: uuid.UUID | None
-
-
-class SetDefaultSSHKeyRequest(BaseModel):
-    ssh_key_id: uuid.UUID
-
 
 @router.post(
     "",
@@ -48,7 +31,7 @@ class SetDefaultSSHKeyRequest(BaseModel):
 )
 async def create_project(
     data: ProjectCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Create a new project.
@@ -61,7 +44,6 @@ async def create_project(
     Returns:
         The newly created project.
     """
-    user = await _get_user(session, user_id)
     project = Project(
         name=data.name,
         description=data.description,
@@ -81,7 +63,7 @@ async def create_project(
     description="Retrieve all projects owned by the authenticated user.",
 )
 async def list_projects(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[Project]:
     """List all projects for the authenticated user.
@@ -93,7 +75,6 @@ async def list_projects(
     Returns:
         List of projects owned by the user.
     """
-    user = await _get_user(session, user_id)
     result = await session.execute(select(Project).where(Project.owner_id == user.id))
     return list(result.scalars().all())
 
@@ -106,7 +87,8 @@ async def list_projects(
 )
 async def get_project(
     project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Get a specific project by ID.
@@ -119,8 +101,8 @@ async def get_project(
     Returns:
         The requested project.
     """
-    await _get_user(session, user_id)
+    return project
-    return await _get_owned_project(project_id, user_id, session)
+
 
 
 @router.patch(
@@ -132,7 +114,8 @@ async def get_project(
 async def update_project(
     project_id: uuid.UUID,
     data: ProjectUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Update a project.
@@ -146,8 +129,6 @@ async def update_project(
     Returns:
         The updated project.
     """
-    await _get_user(session, user_id)
-    project = await _get_owned_project(project_id, user_id, session)
 
     if data.name is not None:
         project.name = data.name
@@ -167,7 +148,8 @@ async def update_project(
 )
 async def delete_project(
     project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
     session: AsyncSession = Depends(get_db_session),
 ) -> Response:
     """Delete a project and all its repositories.
@@ -180,8 +162,6 @@ async def delete_project(
     Returns:
         Empty response with 204 status code.
     """
-    await _get_user(session, user_id)
-    project = await _get_owned_project(project_id, user_id, session)
 
     # Delete repositories from disk and database
     result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
@@ -205,7 +185,8 @@ async def delete_project(
 async def set_default_ssh_key(
     project_id: uuid.UUID,
     data: SetDefaultSSHKeyRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
     session: AsyncSession = Depends(get_db_session),
 ) -> Project:
     """Set the default SSH key for a project.
@@ -219,8 +200,6 @@ async def set_default_ssh_key(
     Returns:
         The updated project.
     """
-    user = await _get_user(session, user_id)
-    project = await _get_owned_project(project_id, user_id, session)
 
     ssh_key = await session.get(SSHKey, data.ssh_key_id)
     if ssh_key is None or ssh_key.user_id != user.id:

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/ssh_keys.py

@@ -1,4 +1,3 @@
-import base64
 import uuid
 from datetime import datetime
 
@@ -6,17 +5,19 @@ from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey
 from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import get_current_user, get_db_session
 from src.config import Settings
 from src.models.ssh_key import SSHKey
+from src.models.user import User
+from src.schemas.ssh_key import SSHKeyCreate, SSHKeyResponse
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 
 
+
 def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
     import base64
@@ -53,36 +54,6 @@ def generate_ssh_key_pair() -> tuple[str, str]:
     return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
 
 
-class SSHKeyCreate(BaseModel):
-    name: str
-
-
-class SSHKeyResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    public_key: str
-    created_at: datetime
-
-
-class SignPayloadRequest(BaseModel):
-    payload: str
-
-
-class SignatureResponse(BaseModel):
-    signature: str
-
-
-class VerifySignatureRequest(BaseModel):
-    payload: str
-    signature: str
-
-
-class VerifySignatureResponse(BaseModel):
-    valid: bool
-
-
 @router.post(
     "",
     response_model=SSHKeyResponse,
@@ -92,7 +63,7 @@ class VerifySignatureResponse(BaseModel):
 )
 async def create_ssh_key(
     data: SSHKeyCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> SSHKey:
     """Create a new SSH key pair.
@@ -105,7 +76,6 @@ async def create_ssh_key(
     Returns:
         The newly created SSH key with public key exposed.
     """
-    user = await _get_user(session, user_id)
     private_key, public_key = generate_ssh_key_pair()
 
     fernet = _get_fernet()
@@ -130,7 +100,7 @@ async def create_ssh_key(
     description="List all SSH keys for the authenticated user.",
 )
 async def list_ssh_keys(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[SSHKey]:
     """List all SSH keys for the authenticated user.
@@ -142,7 +112,6 @@ async def list_ssh_keys(
     Returns:
         List of SSH keys owned by the user.
     """
-    user = await _get_user(session, user_id)
     result = await session.execute(select(SSHKey).where(SSHKey.user_id == user.id))
     return list(result.scalars().all())
 
@@ -155,7 +124,7 @@ async def list_ssh_keys(
 )
 async def delete_ssh_key(
     key_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
     """Delete an SSH key.
@@ -168,87 +137,9 @@ async def delete_ssh_key(
     Returns:
         None with 204 status code.
     """
-    user = await _get_user(session, user_id)
     ssh_key = await session.get(SSHKey, key_id)
     if ssh_key is None or ssh_key.user_id != user.id:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
 
     await session.delete(ssh_key)
     await session.commit()
-
-
-@router.post(
-    "/{key_id}/sign",
-    response_model=SignatureResponse,
-    summary="Sign payload",
-    description="Sign a payload using the SSH private key.",
-)
-async def sign_payload(
-    key_id: uuid.UUID,
-    data: SignPayloadRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> SignatureResponse:
-    """Sign a payload with an SSH key.
-
-    Args:
-        key_id: UUID of the SSH key to use for signing.
-        data: Sign request containing the payload string.
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        Base64-encoded Ed25519 signature.
-    """
-    user = await _get_user(session, user_id)
-    ssh_key = await session.get(SSHKey, key_id)
-    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
-
-    fernet = _get_fernet()
-    private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
-
-    private_key = serialization.load_ssh_private_key(
-        private_key_pem.encode(), password=None
-    )
-
-    signature = private_key.sign(data.payload.encode())
-    return SignatureResponse(signature=base64.b64encode(signature).decode())
-
-
-@router.post(
-    "/{key_id}/verify",
-    response_model=VerifySignatureResponse,
-    summary="Verify signature",
-    description="Verify a signature against a payload using the SSH public key.",
-)
-async def verify_signature(
-    key_id: uuid.UUID,
-    data: VerifySignatureRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> VerifySignatureResponse:
-    """Verify a signature with an SSH key's public key.
-
-    Args:
-        key_id: UUID of the SSH key to use for verification.
-        data: Verify request containing payload and base64-encoded signature.
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        Whether the signature is valid.
-    """
-    user = await _get_user(session, user_id)
-    ssh_key = await session.get(SSHKey, key_id)
-    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
-
-    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
-
-    try:
-        signature = base64.b64decode(data.signature)
-        public_key.verify(signature, data.payload.encode())
-        return VerifySignatureResponse(valid=True)
-    except Exception:
-        return VerifySignatureResponse(valid=False)

apps/api/src/api/terminal.py

@@ -1,102 +1,65 @@
 """WebSocket terminal endpoint for tool instances."""
 
 import asyncio
-import json
 import logging
 import uuid
-from contextlib import suppress
 
-from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
+from fastapi import APIRouter, Depends, WebSocket
-from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from starlette.websockets import WebSocketDisconnect
 
-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import get_db_session
-from src.models.terminal_session import TerminalSessionModel
 from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.services.terminal_manager import terminal_manager
-from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
 
 router = APIRouter()
 logger = logging.getLogger(__name__)
 
 
-class SessionRef:
-    """Mutable reference to a terminal session, allowing updates during reset."""
-
-    def __init__(self, session, slot_session_id: str | None = None):
-        self.session = session
-        self.slot_session_id = slot_session_id or session.session_id
-
-
 @router.websocket(
     "/ws/tool-instances/{instance_id}/terminal",
 )
-async def terminal_websocket_default(
+async def terminal_websocket(
     websocket: WebSocket,
     instance_id: str,
     db_session: AsyncSession = Depends(get_db_session),
 ) -> None:
-    """WebSocket endpoint for terminal access (default session alias).
+    """WebSocket endpoint for terminal access to a tool instance.
 
-    Backward-compatible route that maps to the default session.
+    Provides an interactive terminal session inside a running tool instance container.
-    """
+    Supports:
-    await _handle_terminal_websocket(websocket, instance_id, None, db_session)
+    - Auto-reconnection (client reconnects, server spawns new session)
-
+    - Heartbeat ping/pong
-
+    - Binary and text input frames
-@router.websocket(
+    - Graceful session end notifications
-    "/ws/tool-instances/{instance_id}/terminal/{session_id}",
-)
-async def terminal_websocket_specific(
-    websocket: WebSocket,
-    instance_id: str,
-    session_id: str,
-    db_session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """WebSocket endpoint for a specific terminal session."""
-    await _handle_terminal_websocket(websocket, instance_id, session_id, db_session)
-
-
-async def _handle_terminal_websocket(
-    websocket: WebSocket,
-    instance_id: str,
-    target_session_id: str | None,
-    db_session: AsyncSession,
-) -> None:
-    """Shared WebSocket handler for terminal sessions.
 
     Args:
         websocket: The WebSocket connection.
         instance_id: UUID string of the tool instance.
-        target_session_id: Specific session ID (slot key). None means default session.
         db_session: Database session.
+
+    Returns:
+        None. Communicates via WebSocket messages.
+
     """
-    logger.debug(
+    logger.info("Terminal WebSocket connection attempt for instance %s", instance_id)
-        "Terminal WebSocket connection attempt for instance %s (session=%s)",
-        instance_id,
-        target_session_id or "default",
-    )
     await websocket.accept()
-    logger.debug("Terminal WebSocket accepted for instance %s", instance_id)
 
     try:
-        # Parse instance_id
         instance_uuid = uuid.UUID(instance_id)
     except ValueError:
         logger.error("Invalid instance ID: %s", instance_id)
         await websocket.close(code=4001, reason="Invalid instance ID")
         return
 
-    # Authenticate user from session cookie
     user_id = await _get_user_from_websocket(websocket, db_session)
     if user_id is None:
         logger.warning(
-            "Unauthorized terminal access attempt for instance %s", instance_id
+            "Unauthorized terminal access attempt for instance %s",
+            instance_id,
         )
         await websocket.close(code=4003, reason="Unauthorized")
         return
 
-    # Get instance and verify ownership
     instance = await db_session.get(ToolInstance, instance_uuid)
     if instance is None:
         logger.warning("Instance %s not found", instance_id)
@@ -122,624 +85,50 @@ async def _handle_terminal_websocket(
         await websocket.close(code=4004, reason="Instance not running")
         return
 
-    logger.debug("Terminal auth passed for instance %s, user %s", instance_id, user_id)
+    logger.info(
-
+        "Creating terminal session for instance %s (container_id=%s)",
-    # Verify the container actually exists (may have been removed/recreated)
+        instance_id,
-    from src.services.docker import get_container_status
+        instance.container_id,
-
+    )
-    container_status = get_container_status(instance.container_id)
-    if container_status["status"] == "not_found":
-        logger.error(
-            "Container %s for instance %s not found (may have been removed)",
-            instance.container_id,
-            instance_id,
-        )
-        await websocket.close(
-            code=4004, reason="Container not found — restart the tool instance"
-        )
-        return
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-    if startup_command:
-        logger.debug(
-            "Using startup command for instance %s: %s",
-            instance_id,
-            startup_command,
-        )
-
-    session = None
-
-    # Get or create terminal session
     try:
-        if target_session_id is None:
+        session = await terminal_manager.create_session(
-            # Default session alias
+            instance_uuid,
-            session = await terminal_manager.get_or_create_session(
+            instance.container_id,
-                instance_uuid,
+            websocket,
-                instance.container_id,
+        )
-                startup_command=startup_command,
+        logger.info(
-            )
+            "Terminal session created successfully for instance %s",
-            slot_session_id = "default"
+            instance_id,
-        else:
-            # Specific session
-            session = terminal_manager.get_session(
-                instance_id,
-                target_session_id,
-            )
-            if session is None:
-                # Session not in memory — may have been lost on server restart.
-                # Try to restore from the DB row.
-                db_row = await db_session.get(
-                    TerminalSessionModel, uuid.UUID(target_session_id)
-                )
-                if (
-                    db_row is not None
-                    and db_row.instance_id == instance_uuid
-                    and db_row.status != "closed"
-                ):
-                    logger.info(
-                        "Restoring terminal session %s for instance %s from DB",
-                        target_session_id,
-                        instance_id,
-                    )
-                    session = await terminal_manager.create_session(
-                        instance_uuid,
-                        instance.container_id,
-                        startup_command=startup_command,
-                        name=db_row.name,
-                        session_id=target_session_id,
-                    )
-                else:
-                    logger.warning(
-                        "Session %s not found for instance %s",
-                        target_session_id,
-                        instance_id,
-                    )
-                    await websocket.close(code=4004, reason="Session not found")
-                    return
-            # Determine slot key for reset scoping
-            key = terminal_manager._find_key_by_internal_id(
-                instance_id, session.session_id
-            )
-            slot_session_id = key[1] if key else target_session_id
-
-        logger.debug(
-            "Terminal session ready for instance %s (session_id=%s, slot=%s)",
-            instance_id,
-            session.session_id,
-            slot_session_id,
         )
-
-        # Attach WebSocket to session
-        await terminal_manager.attach_websocket(session, websocket)
-        logger.debug("WebSocket attached to session for instance %s", instance_id)
 
         # Send connected status
         await websocket.send_json({"type": "status", "status": "connected"})
-        logger.debug("Sent connected status for instance %s", instance_id)
 
-        # Use mutable session reference so loops can survive reset
+        # Monitor session health and echo state
-        session_ref = SessionRef(session, slot_session_id)
+        while session.is_alive() and not session.closed:
-
+            # Check echo state periodically
-        # Start I/O loops and heartbeat
+            new_echo_state = await session.check_echo_state()
-        read_task = asyncio.create_task(_read_loop(session_ref, websocket))
+            if new_echo_state is not None:
-        write_task = asyncio.create_task(
+                await websocket.send_json(
-            _write_loop(session_ref, websocket, instance_id)
+                    {"type": "set_echo_state", "enabled": new_echo_state},
-        )
-        heartbeat_task = asyncio.create_task(_heartbeat_loop(websocket))
-        logger.debug("Started terminal loops for instance %s", instance_id)
-
-        # Wait for either task to complete (indicating disconnect or error)
-        done, pending = await asyncio.wait(
-            [read_task, write_task, heartbeat_task],
-            return_when=asyncio.FIRST_COMPLETED,
-        )
-
-        logger.debug(
-            "Terminal loop completed for instance %s, done=%s",
-            instance_id,
-            len(done),
-        )
-
-        # Cancel remaining tasks
-        for task in pending:
-            task.cancel()
-
-    except WebSocketDisconnect:
-        logger.debug("WebSocket disconnected for instance %s", instance_id)
-    except Exception as exc:
-        logger.error(
-            "Terminal session error for instance %s: %s",
-            instance_id,
-            str(exc),
-            exc_info=True,
-        )
-        with suppress(Exception):
-            await websocket.close(code=4000, reason=f"Error: {exc}")
-    finally:
-        # Detach WebSocket, don't kill session
-        with suppress(Exception):
-            if session is not None:
-                await terminal_manager.detach_websocket(session, websocket)
-                logger.debug(
-                    "WebSocket detached from session for instance %s", instance_id
                 )
+            await asyncio.sleep(1.0)
 
+        # Session ended — determine reason and notify client
+        exit_reason = session.get_exit_reason() or "process_exit"
+        await websocket.send_json({"type": "session_ended", "reason": exit_reason})
+        await websocket.close(code=1000, reason=f"Session ended: {exit_reason}")
 
-async def _read_loop(session_ref: SessionRef, websocket) -> None:
-    """Read output from the container and send to WebSocket."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            data = await session.read_output()
-            if data:
-                try:
-                    await websocket.send_bytes(data)
-                except WebSocketDisconnect:
-                    break
-                except Exception:
-                    break
-            else:
-                await asyncio.sleep(0.01)
     except Exception:
+        logger.exception(
+            "Terminal session error for instance %s",
+            instance_id,
+        )
+        await websocket.close(code=4000, reason="Terminal session error")
+    finally:
         pass
 
 
-async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
-    """Read input from WebSocket and send to container."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            message = await websocket.receive()
-            if message["type"] == "websocket.receive":
-                if "bytes" in message:
-                    await session.write_input(message["bytes"])
-                elif "text" in message:
-                    text = message["text"]
-                    if text.startswith("{"):
-                        # Control message (JSON)
-                        try:
-                            ctrl = json.loads(text)
-                            msg_type = ctrl.get("type")
-
-                            if msg_type == "resize":
-                                cols = ctrl.get("cols", 80)
-                                rows = ctrl.get("rows", 24)
-                                logger.debug(
-                                    "Received resize message for instance %s: %sx%s",
-                                    instance_id,
-                                    cols,
-                                    rows,
-                                )
-                                await session.resize(cols, rows)
-                            elif msg_type == "reset":
-                                # Reset terminal session (scoped to current slot)
-                                logger.debug(
-                                    "Resetting terminal session for instance %s (slot=%s)",
-                                    session.instance_id,
-                                    session_ref.slot_session_id,
-                                )
-                                await websocket.send_json(
-                                    {"type": "status", "status": "resetting"}
-                                )
-
-                                # Reset the session scoped to its slot
-                                new_session = await terminal_manager.reset_session(
-                                    session.instance_id,
-                                    session.container_id,
-                                    startup_command=session.startup_command,
-                                    session_id=session_ref.slot_session_id,
-                                    name=session.name,
-                                )
-
-                                # Update the mutable session reference
-                                session_ref.session = new_session
-
-                                # Attach to new session
-                                await terminal_manager.attach_websocket(
-                                    new_session, websocket
-                                )
-                                await websocket.send_json(
-                                    {"type": "status", "status": "connected"}
-                                )
-
-                                # Continue the loop with the new session
-                                continue
-
-                        except json.JSONDecodeError:
-                            # Not a valid JSON control message, treat as regular input
-                            await session.write_input(text.encode("utf-8"))
-                    else:
-                        await session.write_input(text.encode("utf-8"))
-            elif message["type"] == "websocket.disconnect":
-                break
-    except Exception:
-        pass
-
-
-async def _heartbeat_loop(websocket: WebSocket) -> None:
-    """Send periodic ping messages to detect disconnections."""
-    try:
-        while True:
-            await asyncio.sleep(30)  # Ping every 30 seconds
-            try:
-                await websocket.send_json({"type": "ping"})
-            except Exception:
-                # WebSocket is closed or broken
-                break
-    except Exception:
-        pass
-
-
-async def _get_terminal_instance(
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID,
-    db_session: AsyncSession,
-) -> ToolInstance:
-    """Fetch instance and validate auth, ownership, and running status.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        The validated ToolInstance.
-
-    Raises:
-        HTTPException: If instance not found, not owned, or not running.
-    """
-    instance = await db_session.get(ToolInstance, instance_id)
-    if instance is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Instance not found"
-        )
-
-    if instance.owner_id != user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="Not authorized to access this instance",
-        )
-
-    if instance.status != "running" or not instance.container_id:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST, detail="Instance is not running"
-        )
-
-    return instance
-
-
-@router.get(
-    "/instances/{instance_id}/terminal/sessions",
-    summary="List terminal sessions",
-    description="List terminal sessions for a tool instance with live WebSocket state.",
-)
-async def list_terminal_sessions(
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List terminal sessions for an instance.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with sessions list.
-    """
-    await _get_terminal_instance(instance_id, user_id, db_session)
-
-    # Query active DB rows for this instance
-    result = await db_session.execute(
-        select(TerminalSessionModel)
-        .where(TerminalSessionModel.instance_id == instance_id)
-        .where(TerminalSessionModel.status != "closed")
-        .order_by(TerminalSessionModel.created_at.asc())
-    )
-    db_rows = result.scalars().all()
-
-    # Build response with live has_websockets flag.
-    # Include DB rows even without in-memory counterparts (e.g. after
-    # server restart) so the frontend can display tabs and reconnect.
-    sessions = []
-    for row in db_rows:
-        live_session = terminal_manager.get_session(str(instance_id), str(row.id))
-        sessions.append(
-            {
-                "id": str(row.id),
-                "name": row.name,
-                "status": row.status,
-                "has_websockets": live_session.has_websockets()
-                if live_session
-                else False,
-                "created_at": row.created_at.isoformat() if row.created_at else None,
-                "last_activity_at": row.last_activity_at.isoformat()
-                if row.last_activity_at
-                else None,
-            }
-        )
-
-    return {"sessions": sessions}
-
-
-@router.post(
-    "/instances/{instance_id}/terminal/sessions",
-    summary="Create terminal session",
-    description="Create a new terminal session for a running tool instance.",
-    status_code=status.HTTP_201_CREATED,
-)
-async def create_terminal_session(
-    instance_id: uuid.UUID,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new terminal session.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        data: Request body with optional name.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with new session details.
-
-    Raises:
-        HTTPException: 409 if max sessions reached.
-    """
-    instance = await _get_terminal_instance(instance_id, user_id, db_session)
-    assert instance.container_id is not None
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-
-    name = data.get("name")
-
-    try:
-        session = await terminal_manager.create_session(
-            instance_id,
-            instance.container_id,
-            startup_command=startup_command,
-            name=name,
-        )
-    except MaxSessionsExceededError:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail="Maximum of 5 terminal sessions reached for this instance",
-        ) from None
-
-    return {
-        "id": session.session_id,
-        "name": session.name,
-        "status": session.status,
-        "created_at": session.last_activity,
-    }
-
-
-@router.delete(
-    "/instances/{instance_id}/terminal/sessions/{session_id}",
-    summary="Close terminal session",
-    description="Close a specific terminal session.",
-)
-async def close_terminal_session(
-    instance_id: uuid.UUID,
-    session_id: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Close a terminal session.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        session_id: ID of the session to close.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with closure status.
-    """
-    await _get_terminal_instance(instance_id, user_id, db_session)
-
-    # Find the session by internal ID to determine its slot key
-    key = terminal_manager._find_key_by_internal_id(str(instance_id), session_id)
-    if (
-        key is None
-        and terminal_manager.get_session(str(instance_id), session_id) is not None
-    ):
-        key = (str(instance_id), session_id)
-
-    if key is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
-        )
-
-    await terminal_manager.close_session(key[0], key[1])
-
-    return {"status": "closed", "session_id": session_id}
-
-
-@router.post(
-    "/instances/{instance_id}/terminal/sessions/{session_id}/reset",
-    summary="Reset terminal session",
-    description="Reset a specific terminal session, killing the current shell and starting fresh.",
-)
-async def reset_specific_terminal_session(
-    instance_id: uuid.UUID,
-    session_id: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Reset a specific terminal session.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        session_id: ID of the session to reset.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with reset session details.
-    """
-    instance = await _get_terminal_instance(instance_id, user_id, db_session)
-    assert instance.container_id is not None
-
-    # Determine slot key for reset
-    key = terminal_manager._find_key_by_internal_id(str(instance_id), session_id)
-    if (
-        key is None
-        and terminal_manager.get_session(str(instance_id), session_id) is not None
-    ):
-        key = (str(instance_id), session_id)
-
-    if key is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
-        )
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-
-    # Preserve name if possible
-    live_session = terminal_manager.get_session(str(instance_id), session_id)
-    name = live_session.name if live_session else None
-
-    new_session = await terminal_manager.reset_session(
-        instance_id,
-        instance.container_id,
-        startup_command=startup_command,
-        session_id=key[1],
-        name=name,
-    )
-
-    return {
-        "id": new_session.session_id,
-        "name": new_session.name,
-        "status": new_session.status,
-    }
-
-
-@router.post(
-    "/instances/{instance_id}/terminal/sessions/{session_id}/rename",
-    summary="Rename terminal session",
-    description="Rename a specific terminal session.",
-)
-async def rename_terminal_session(
-    instance_id: uuid.UUID,
-    session_id: str,
-    data: dict,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Rename a terminal session.
-
-    Args:
-        instance_id: UUID of the tool instance.
-        session_id: ID of the session to rename.
-        data: Request body with new name.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with updated session details.
-    """
-    await _get_terminal_instance(instance_id, user_id, db_session)
-
-    new_name = data.get("name")
-    if not new_name or not isinstance(new_name, str):
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST, detail="Name is required"
-        )
-
-    # Update in-memory session name if live
-    live_session = terminal_manager.get_session(str(instance_id), session_id)
-    if live_session:
-        live_session.name = new_name
-
-    # Update DB row
-    db_row = await db_session.get(TerminalSessionModel, uuid.UUID(session_id))
-    if db_row is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
-        )
-
-    db_row.name = new_name
-    await db_session.commit()
-
-    return {"id": str(db_row.id), "name": new_name}
-
-
-@router.post(
-    "/instances/{instance_id}/terminal/reset",
-    summary="Reset terminal session (legacy alias)",
-    description="Reset the default terminal session for a tool instance. Preserved for backward compatibility.",
-)
-async def reset_terminal_session(
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Reset the default terminal session for an instance (legacy alias).
-
-    Args:
-        instance_id: UUID of the tool instance.
-        user_id: ID of the authenticated user.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with status message.
-    """
-    instance = await _get_terminal_instance(instance_id, user_id, db_session)
-    assert instance.container_id is not None
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-
-    try:
-        # Reset the default session
-        new_session = await terminal_manager.reset_session(
-            instance_id,
-            instance.container_id,
-            startup_command=startup_command,
-        )
-
-        logger.info(
-            "Terminal session reset for instance %s (new session_id=%s)",
-            instance_id,
-            new_session.session_id,
-        )
-
-        return {
-            "status": "success",
-            "message": "Terminal session reset successfully",
-            "instance_id": str(instance_id),
-            "session_id": new_session.session_id,
-        }
-    except Exception as exc:
-        logger.error(
-            "Failed to reset terminal session for instance %s: %s",
-            instance_id,
-            str(exc),
-            exc_info=True,
-        )
-        raise HTTPException(
-            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Failed to reset terminal session: {exc}",
-        ) from exc
-
-
 async def _get_user_from_websocket(
     websocket: WebSocket,
     db_session: AsyncSession,
@@ -752,6 +141,7 @@ async def _get_user_from_websocket(
 
     Returns:
         The user's UUID if authenticated, None otherwise.
+
     """
     from src.auth.session import decode_session_cookie
     from src.config import Settings

apps/api/src/api/tool_configs.py

@@ -0,0 +1,213 @@
+"""Tool configuration API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+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_config import ToolConfig
+from src.models.tool_type import ToolType
+from src.schemas.tool_config import ToolConfigCreate, ToolConfigUpdate, ToolConfigResponse
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/tool-configs", tags=["tool-configs"])
+
+
+@router.get("", summary="List tool configs", description="Get all tool configs for the current user.")
+async def list_configs(
+    tool_type_id: str | None = None,
+    project_id: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list:
+    """List tool configs for the current user."""
+    query = select(ToolConfig).where(ToolConfig.user_id == user_id)
+    
+    if tool_type_id:
+        query = query.where(ToolConfig.tool_type_id == uuid.UUID(tool_type_id))
+    if project_id:
+        query = query.where(ToolConfig.project_id == uuid.UUID(project_id))
+    else:
+        # If no project specified, get only global configs (project_id is None)
+        query = query.where(ToolConfig.project_id.is_(None))
+    
+    result = await session.execute(query)
+    configs = result.scalars().all()
+    
+    return [
+        {
+            "id": str(c.id),
+            "tool_type_id": str(c.tool_type_id),
+            "project_id": str(c.project_id) if c.project_id else None,
+            "key": c.key,
+            "value": c.value,
+            "config_type": c.config_type,
+            "file_path": c.file_path,
+            "port_override": c.port_override,
+            "start_command": c.start_command,
+            "working_directory": c.working_directory,
+            "environment_variables": c.environment_variables,
+            "volumes": c.volumes,
+        }
+        for c in configs
+    ]
+
+
+@router.post("", summary="Create tool config", description="Create a new tool config.", status_code=status.HTTP_201_CREATED)
+async def create_config(
+    data: ToolConfigCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a tool config."""
+    # Verify tool type exists
+    tool_type = await session.get(ToolType, uuid.UUID(data.tool_type_id))
+    if tool_type is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    
+    # Check for existing config with same key
+    query = select(ToolConfig).where(
+        ToolConfig.user_id == user_id,
+        ToolConfig.tool_type_id == uuid.UUID(data.tool_type_id),
+        ToolConfig.key == data.key,
+    )
+    if data.project_id:
+        query = query.where(ToolConfig.project_id == uuid.UUID(data.project_id))
+    else:
+        query = query.where(ToolConfig.project_id.is_(None))
+    
+    existing = await session.scalar(query)
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config with key '{data.key}' already exists"
+        )
+    
+    config = ToolConfig(
+        user_id=user_id,
+        tool_type_id=uuid.UUID(data.tool_type_id),
+        project_id=uuid.UUID(data.project_id) if data.project_id else None,
+        key=data.key,
+        value=data.value,
+        config_type=data.config_type,
+        file_path=data.file_path,
+        port_override=data.port_override,
+        start_command=data.start_command,
+        working_directory=data.working_directory,
+        environment_variables=data.environment_variables,
+        volumes=data.volumes,
+    )
+    session.add(config)
+    await session.commit()
+    await session.refresh(config)
+    
+    return {
+        "id": str(config.id),
+        "tool_type_id": str(config.tool_type_id),
+        "project_id": str(config.project_id) if config.project_id else None,
+        "key": config.key,
+        "value": config.value,
+        "config_type": config.config_type,
+        "file_path": config.file_path,
+        "port_override": config.port_override,
+        "start_command": config.start_command,
+        "working_directory": config.working_directory,
+        "environment_variables": config.environment_variables,
+        "volumes": config.volumes,
+    }
+
+
+@router.put("/{config_id}", summary="Update tool config", description="Update an existing tool config.")
+async def update_config(
+    config_id: uuid.UUID,
+    data: ToolConfigUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a tool config."""
+    config = await session.get(ToolConfig, config_id)
+    if config is None or config.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
+    
+    if data.key is not None:
+        config.key = data.key
+    if data.value is not None:
+        config.value = data.value
+    if data.config_type is not None:
+        config.config_type = data.config_type
+    if data.file_path is not None:
+        config.file_path = data.file_path
+    if data.port_override is not None:
+        config.port_override = data.port_override
+    if data.start_command is not None:
+        config.start_command = data.start_command
+    if data.working_directory is not None:
+        config.working_directory = data.working_directory
+    if data.environment_variables is not None:
+        config.environment_variables = data.environment_variables
+    if data.volumes is not None:
+        config.volumes = data.volumes
+    
+    await session.commit()
+    await session.refresh(config)
+    
+    return {
+        "id": str(config.id),
+        "tool_type_id": str(config.tool_type_id),
+        "project_id": str(config.project_id) if config.project_id else None,
+        "key": config.key,
+        "value": config.value,
+        "config_type": config.config_type,
+        "file_path": config.file_path,
+        "port_override": config.port_override,
+        "start_command": config.start_command,
+        "working_directory": config.working_directory,
+        "environment_variables": config.environment_variables,
+        "volumes": config.volumes,
+    }
+
+
+@router.get("/defaults/{tool_type_id}", summary="Get default configs", description="Get suggested default configs for a tool type.")
+async def get_default_configs(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get suggested default configs for a tool type."""
+    tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
+    if tool_type is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    
+    # Return suggested defaults based on required_variables
+    defaults = []
+    for var in tool_type.required_variables:
+        defaults.append({
+            "key": var,
+            "value": "",
+            "config_type": "env",
+            "description": f"Required variable: {var}",
+        })
+    
+    return {
+        "tool_type_id": tool_type_id,
+        "suggested_configs": defaults,
+    }
+
+
+@router.delete("/{config_id}", summary="Delete tool config", description="Delete a tool config.")
+async def delete_config(
+    config_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a tool config."""
+    config = await session.get(ToolConfig, config_id)
+    if config is None or config.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
+    
+    await session.delete(config)
+    await session.commit()

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.py

@@ -1,19 +1,15 @@
 import uuid
 from datetime import datetime
 
+import yaml
 from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.api.tool_types_validation import (
+from src.auth.dependencies import get_current_user, get_db_session
-    check_port_exposed,
-    validate_compose_yaml,
-    validate_required_variables,
-)
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.tool_type import ToolType
 from src.models.user import User
+from src.schemas.tool_type import ToolTypeCreate, ToolTypeResponse, ToolTypeUpdate, ToolTypeValidateRequest
 
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
 
@@ -29,237 +25,6 @@ async def _require_admin(user: User) -> None:
     pass
 
 
-class ToolTypeCreate(BaseModel):
-    name: str
-    display_name: str
-    description: str | None = None
-    default_port: int = 0
-    definition_type: str = "compose"
-    manifest_id: uuid.UUID | None = None
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] = []
-    category: str = "other"
-    interface_type: str = "web"
-    requires_port: bool = True
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str) -> str:
-        if v not in ("compose", "dockerfile", "manifest"):
-            raise ValueError(
-                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
-            )
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-
-        if v is None or not v.strip():
-            raise ValueError(
-                "compose_template is required when definition_type is 'compose'"
-            )
-
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "dockerfile":
-            return v
-
-        if v is None or not v.strip():
-            raise ValueError(
-                "dockerfile_template is required when definition_type is 'dockerfile'"
-            )
-
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str) -> str:
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("default_port")
-    @classmethod
-    def validate_default_port(cls, v: int, info) -> int:
-        data = info.data
-        requires_port = data.get("requires_port", True)
-        if not requires_port:
-            return v
-        if v <= 0 or v > 65535:
-            raise ValueError("Port must be between 1 and 65535")
-        return v
-
-    @field_validator("required_variables")
-    @classmethod
-    def validate_required_variables(cls, v: list[str], info) -> list[str]:
-        if not v:
-            return v
-
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-
-        template = data.get("compose_template")
-        if not template:
-            return v
-
-        for var in v:
-            placeholder = f"{{{{{var}}}}}"
-            if placeholder not in template:
-                raise ValueError(
-                    f"Required variable '{var}' not found in compose template"
-                )
-
-        return v
-
-    @model_validator(mode="after")
-    def validate_templates(self) -> "ToolTypeCreate":
-        if self.definition_type == "manifest":
-            if self.manifest_id is None:
-                raise ValueError(
-                    "manifest_id is required when definition_type is 'manifest'"
-                )
-            return self
-
-        if self.definition_type == "dockerfile" and (
-            self.dockerfile_template is None or not self.dockerfile_template.strip()
-        ):
-            raise ValueError(
-                "dockerfile_template is required when definition_type is 'dockerfile'"
-            )
-        if self.definition_type == "compose" and (
-            self.compose_template is None or not self.compose_template.strip()
-        ):
-            raise ValueError(
-                "compose_template is required when definition_type is 'compose'"
-            )
-
-        # Validate that default_port is exposed in compose template (only if requires_port)
-        if (
-            self.requires_port
-            and self.definition_type == "compose"
-            and self.compose_template
-        ):
-            try:
-                parsed = validate_compose_yaml(self.compose_template)
-            except ValueError:
-                return self
-
-            if not check_port_exposed(parsed, self.default_port):
-                raise ValueError(
-                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
-                )
-
-        return self
-
-
-class ToolTypeUpdate(BaseModel):
-    display_name: str | None = None
-    description: str | None = None
-    default_port: int | None = None
-    definition_type: str | None = None
-    manifest_id: uuid.UUID | None = None
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] | None = None
-    category: str | None = None
-    interface_type: str | None = None
-    requires_port: bool | None = None
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("compose", "dockerfile", "manifest"):
-            raise ValueError(
-                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
-            )
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "compose":
-            return v
-
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "dockerfile":
-            return v
-
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-
-        return v
-
-
-class ToolTypeResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    display_name: str
-    description: str | None
-    category: str
-    interface_type: str
-    requires_port: bool
-    default_port: int
-    definition_type: str
-    manifest_id: uuid.UUID | None
-    compose_template: str | None
-    dockerfile_template: str | None
-    build_context: dict | None
-    readiness_probe: dict | None
-    startup_command: str | None
-    required_variables: list[str]
-    created_by_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
 @router.post(
     "",
     response_model=ToolTypeResponse,
@@ -269,7 +34,7 @@ class ToolTypeResponse(BaseModel):
 )
 async def create_tool_type(
     data: ToolTypeCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Create a new tool type.
@@ -282,16 +47,12 @@ async def create_tool_type(
     Returns:
         The newly created tool type.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
     
     # Check for duplicate name
     existing = await session.scalar(select(ToolType).where(ToolType.name == data.name))
     if existing:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_409_CONFLICT, detail="tool type with this name already exists")
-            status_code=status.HTTP_409_CONFLICT,
-            detail="tool type with this name already exists",
-        )
     
     tool_type = ToolType(
         name=data.name,
@@ -299,16 +60,14 @@ async def create_tool_type(
         description=data.description,
         default_port=data.default_port,
         definition_type=data.definition_type,
-        manifest_id=data.manifest_id,
         compose_template=data.compose_template,
         dockerfile_template=data.dockerfile_template,
         build_context=data.build_context,
         readiness_probe=data.readiness_probe,
-        startup_command=data.startup_command,
         required_variables=data.required_variables,
         category=data.category,
-        interface_type=data.interface_type,
+        interfaces=data.interfaces,
-        requires_port=data.requires_port,
+        is_builtin=False,
         created_by_id=user.id,
     )
     session.add(tool_type)
@@ -324,7 +83,7 @@ async def create_tool_type(
     description="List all available tool types including built-in and custom ones.",
 )
 async def list_tool_types(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[ToolType]:
     """List all tool types.
@@ -336,7 +95,6 @@ async def list_tool_types(
     Returns:
         List of all tool types ordered by name.
     """
-    await _get_user(session, user_id)
     result = await session.execute(select(ToolType).order_by(ToolType.name))
     return list(result.scalars().all())
 
@@ -349,7 +107,7 @@ async def list_tool_types(
 )
 async def get_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Get a specific tool type by ID.
@@ -362,12 +120,9 @@ async def get_tool_type(
     Returns:
         The requested tool type.
     """
-    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
-        )
     return tool_type
 
 
@@ -380,7 +135,7 @@ async def get_tool_type(
 async def update_tool_type(
     tool_type_id: uuid.UUID,
     data: ToolTypeUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Update a tool type.
@@ -394,27 +149,24 @@ async def update_tool_type(
     Returns:
         The updated tool type.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
     
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
-        )
     
-    # Built-in tool types can now be modified
+    if tool_type.is_builtin:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="cannot modify built-in tool types")
     
     update_data = data.model_dump(exclude_unset=True)
     
     # Validate port if being updated
-    requires_port = update_data.get("requires_port", tool_type.requires_port)
+    if "default_port" in update_data:
-    if "default_port" in update_data and requires_port:
         new_port = update_data["default_port"]
         if new_port <= 0 or new_port > 65535:
             raise HTTPException(
                 status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Port must be between 1 and 65535",
+                detail="Port must be between 1 and 65535"
             )
         
         # Only validate port exposure for compose definitions
@@ -423,35 +175,53 @@ async def update_tool_type(
             template = update_data.get("compose_template", tool_type.compose_template)
             if template:
                 try:
-                    parsed = validate_compose_yaml(template)
+                    parsed = yaml.safe_load(template)
-                    if not check_port_exposed(parsed, new_port):
+                except yaml.YAMLError:
+                    parsed = None
+                
+                if parsed and isinstance(parsed, dict) and "services" in parsed:
+                    port_str = str(new_port)
+                    port_exposed = 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:
+                                    port_exposed = True
+                                    break
+                                elif isinstance(port_mapping, int) and port_mapping == new_port:
+                                    port_exposed = True
+                                    break
+                        if port_exposed:
+                            break
+                    
+                    if not port_exposed:
                         raise HTTPException(
                             status_code=status.HTTP_400_BAD_REQUEST,
-                            detail=f"Port {new_port} is not exposed in the compose template",
+                            detail=f"Port {new_port} is not exposed in the compose template"
                         )
-                except ValueError as e:
-                    raise HTTPException(
-                        status_code=status.HTTP_400_BAD_REQUEST, detail=str(e)
-                    )
     
     # Validate required variables for compose definitions
     definition_type = update_data.get("definition_type", tool_type.definition_type)
     if definition_type == "compose":
         if "required_variables" in update_data and "compose_template" in update_data:
-            validate_required_variables(
+            template = update_data["compose_template"]
-                update_data["compose_template"], update_data["required_variables"]
+            for var in update_data["required_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"
+                    )
         elif "required_variables" in update_data:
             template = tool_type.compose_template
             if template:
-                validate_required_variables(template, update_data["required_variables"])
+                for var in update_data["required_variables"]:
-
+                    placeholder = f"{{{{{var}}}}}"
-    # When switching to manifest, clear legacy templates
+                    if placeholder not in template:
-    if definition_type == "manifest":
+                        raise HTTPException(
-        if "manifest_id" in update_data:
+                            status_code=status.HTTP_400_BAD_REQUEST,
-            tool_type.manifest_id = update_data["manifest_id"]
+                            detail=f"Required variable '{var}' not found in compose template"
-        tool_type.compose_template = None
+                        )
-        tool_type.dockerfile_template = None
     
     for field, value in update_data.items():
         setattr(tool_type, field, value)
@@ -461,12 +231,6 @@ async def update_tool_type(
     return tool_type
 
 
-class ToolTypeValidateRequest(BaseModel):
-    definition_type: str
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-
-
 @router.post(
     "/validate",
     summary="Validate tool type template",
@@ -474,7 +238,7 @@ class ToolTypeValidateRequest(BaseModel):
 )
 async def validate_tool_type_template(
     data: ToolTypeValidateRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type template syntax.
@@ -487,7 +251,6 @@ async def validate_tool_type_template(
     Returns:
         Validation result with success status and any errors.
     """
-    await _get_user(session, user_id)
 
     errors = []
 
@@ -496,9 +259,15 @@ async def validate_tool_type_template(
             errors.append("Compose template is required")
         else:
             try:
-                validate_compose_yaml(data.compose_template)
+                parsed = yaml.safe_load(data.compose_template)
-            except ValueError as e:
+                if not isinstance(parsed, dict):
-                errors.append(str(e))
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
 
     elif data.definition_type == "dockerfile":
         if not data.dockerfile_template:
@@ -506,11 +275,8 @@ async def validate_tool_type_template(
         elif not data.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
 
-    elif data.definition_type == "manifest":
-        pass  # Manifest validation is handled separately
-
     else:
-        errors.append("definition_type must be 'compose', 'dockerfile', or 'manifest'")
+        errors.append("definition_type must be 'compose' or 'dockerfile'")
 
     return {
         "valid": len(errors) == 0,
@@ -525,7 +291,7 @@ async def validate_tool_type_template(
 )
 async def validate_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type's template syntax.
@@ -538,12 +304,9 @@ async def validate_tool_type(
     Returns:
         Validation result with success status and any errors.
     """
-    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
-        )
     
     errors = []
     
@@ -552,9 +315,15 @@ async def validate_tool_type(
             errors.append("Compose template is empty")
         else:
             try:
-                validate_compose_yaml(tool_type.compose_template)
+                parsed = yaml.safe_load(tool_type.compose_template)
-            except ValueError as e:
+                if not isinstance(parsed, dict):
-                errors.append(str(e))
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
     
     elif tool_type.definition_type == "dockerfile":
         if not tool_type.dockerfile_template:
@@ -562,10 +331,6 @@ async def validate_tool_type(
         elif not tool_type.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
     
-    elif tool_type.definition_type == "manifest":
-        if not tool_type.manifest_id:
-            errors.append("Manifest reference is missing")
-
     return {
         "valid": len(errors) == 0,
         "errors": errors,
@@ -580,7 +345,7 @@ async def validate_tool_type(
 )
 async def delete_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
     """Delete a tool type.
@@ -593,16 +358,14 @@ async def delete_tool_type(
     Returns:
         None with 204 status code.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
     
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
-        )
     
-    # Built-in tool types can now be deleted
+    if tool_type.is_builtin:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="cannot delete built-in tool types")
     
     await session.delete(tool_type)
     await session.commit()

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/user_config.py

@@ -1,22 +1,20 @@
 import logging
 import uuid
 
-from fastapi import APIRouter, Depends
+from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+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.schemas.user_config import UserConfigResponse, UserConfigUpdate
-logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
-async def _get_or_create_config(
+
-    session: AsyncSession, user_id: uuid.UUID
+async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
-) -> UserConfig:
     """Get or create user config record.
 
     Args:
@@ -26,40 +24,16 @@ async def _get_or_create_config(
     Returns:
         The user's config, creating a new one if it doesn't exist.
     """
-    result = await session.execute(
+    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user.id))
-        select(UserConfig).where(UserConfig.user_id == user_id)
-    )
     config = result.scalar_one_or_none()
     if config is None:
-        config = UserConfig(user_id=user_id, config={})
+        config = UserConfig(user_id=user.id, config={})
         session.add(config)
         await session.commit()
         await session.refresh(config)
     return config
 
 
-class UserConfigResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    default_editor: str | None = None
-    theme: str = "system"
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-    notification_mute_categories: list[str] | None = None
-    notification_toast_level: str | None = None
-
-
-class UserConfigUpdate(BaseModel):
-    default_editor: str | None = None
-    theme: str | None = None
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-    notification_mute_categories: list[str] | None = None
-    notification_toast_level: str | None = None
-
-
 @router.get(
     "/config",
     response_model=UserConfigResponse,
@@ -67,7 +41,7 @@ class UserConfigUpdate(BaseModel):
     description="Get the current user's configuration settings.",
 )
 async def get_user_config(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Get the current user's configuration.
@@ -79,8 +53,7 @@ async def get_user_config(
     Returns:
         The user's configuration settings.
     """
-    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user.id)
-    config = await _get_or_create_config(session, user_id)
     return UserConfigResponse.model_validate(config.config)
 
 
@@ -92,7 +65,7 @@ async def get_user_config(
 )
 async def update_user_config(
     data: UserConfigUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Update the current user's configuration.
@@ -105,16 +78,15 @@ async def update_user_config(
     Returns:
         The updated user configuration.
     """
-    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user.id)
-    config = await _get_or_create_config(session, user_id)
 
     # Merge updates
     update_data = data.model_dump(exclude_unset=True)
-    logger.debug("Updating user config for user %s: %s", user_id, update_data)
+    logger.info("Updating user config for user %s: %s", user.id, update_data)
     # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
     config.config = {**config.config, **update_data}
 
     await session.commit()
     await session.refresh(config)
-    logger.debug("Updated config: %s", config.config)
+    logger.info("Updated config: %s", config.config)
     return UserConfigResponse.model_validate(config.config)

apps/api/src/api/users.py

@@ -2,11 +2,14 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from pydantic import BaseModel, ConfigDict
+from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import get_current_user, get_db_session
+from src.models.tool_instance import ToolInstance
 from src.models.user import User
+from src.schemas.tool_instance import SessionItemResponse, SessionListResponse
+from src.schemas.user import UserProfileResponse, UserProfileUpdate
 
 router = APIRouter(prefix="/users", tags=["users"])
 
@@ -16,19 +19,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-class UserProfileResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    email: str
-    name: str
-    avatar_url: str | None
-
-
-class UserProfileUpdate(BaseModel):
-    name: str | None = None
-    email: str | None = None
-
 
 @router.get(
     "/me",
@@ -37,7 +27,7 @@ class UserProfileUpdate(BaseModel):
     description="Retrieve the profile of the currently authenticated user.",
 )
 async def get_profile(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Get the current user's profile.
@@ -49,7 +39,7 @@ async def get_profile(
     Returns:
         The user's profile information.
     """
-    return await _get_user(session, user_id)
+    return user
 
 
 @router.put(
@@ -60,7 +50,7 @@ async def get_profile(
 )
 async def update_profile(
     data: UserProfileUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Update the current user's profile.
@@ -73,7 +63,6 @@ async def update_profile(
     Returns:
         The updated user profile.
     """
-    user = await _get_user(session, user_id)
 
     if data.name is not None:
         if len(data.name.strip()) == 0:
@@ -98,7 +87,7 @@ async def update_profile(
 )
 async def upload_avatar(
     file: UploadFile,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Upload a profile avatar image.
@@ -111,7 +100,6 @@ async def upload_avatar(
     Returns:
         The updated user profile with new avatar URL.
     """
-    user = await _get_user(session, user_id)
 
     if file.content_type not in ALLOWED_CONTENT_TYPES:
         raise HTTPException(
@@ -146,3 +134,41 @@ async def upload_avatar(
     await session.commit()
     await session.refresh(user)
     return user
+
+
+@router.get(
+    "/me/sessions",
+    response_model=SessionListResponse,
+    summary="Get current user sessions",
+    description="Retrieve all tool instances (sessions) for the authenticated user.",
+)
+async def get_user_sessions(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> SessionListResponse:
+    """Return all tool instances for the current user with related names."""
+    result = await session.execute(
+        select(ToolInstance)
+        .where(ToolInstance.owner_id == user.id)
+        .order_by(ToolInstance.created_at.desc())
+    )
+    instances = result.scalars().all()
+
+    sessions = [
+        SessionItemResponse(
+            id=str(inst.id),
+            display_name=inst.display_name,
+            tool_type_name=inst.tool_type.display_name if inst.tool_type else "Unknown",
+            tool_icon=inst.tool_type.icon if inst.tool_type else None,
+            tool_type_interfaces=inst.tool_type.interfaces if inst.tool_type else [],
+            repository_name=inst.repository.name if inst.repository else "Unknown",
+            repository_id=str(inst.repository_id),
+            project_name=inst.project.name if inst.project else "Unknown",
+            project_id=str(inst.project_id),
+            status=inst.status,
+            url=inst.url,
+        )
+        for inst in instances
+    ]
+
+    return SessionListResponse(sessions=sessions)

apps/api/src/auth/dependencies.py

@@ -50,25 +50,17 @@ async def get_current_user(
     return user
 
 
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+async def get_owned_project(
-    """Fetch a user by ID or raise 401 if not found."""
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
-    return user
-
-
-async def _get_owned_project(
     project_id: uuid.UUID,
-    user_id: uuid.UUID,
+    user: User = Depends(get_current_user),
-    session: AsyncSession,
+    db_session: AsyncSession = Depends(get_db_session),
-) -> "Project":
+) -> Project:
     """Fetch a project and verify ownership.
 
     Args:
-        project_id: UUID of the project.
+        project_id: UUID of the project (injected from path parameter).
-        user_id: ID of the authenticated user.
+        user: The currently authenticated user.
-        session: Database session.
+        db_session: Database session.
 
     Returns:
         The project if found and owned by the user.
@@ -76,11 +68,9 @@ async def _get_owned_project(
     Raises:
         HTTPException: 404 if project not found, 403 if user is not the owner.
     """
-    from src.models.project import Project
+    project = await db_session.get(Project, project_id)
-
-    project = await session.get(Project, project_id)
     if project is None:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="project not found")
-    if project.owner_id != user_id:
+    if project.owner_id != user.id:
         raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
     return project

apps/api/src/logging_config.py

@@ -1,52 +1,15 @@
-"""Structured JSON logging configuration."""
-
-import json
 import logging
 import sys
 import time
 import traceback
-from collections.abc import Callable
+from typing import Callable
 
 from fastapi import Request, Response
 from starlette.middleware.base import BaseHTTPMiddleware
 
-from src.services.correlation import get_correlation_id
-
 logger = logging.getLogger(__name__)
 
 
-class CorrelationIdFilter(logging.Filter):
-    """Inject correlation_id into every log record from context var."""
-
-    def filter(self, record: logging.LogRecord) -> bool:
-        record.correlation_id = get_correlation_id()  # type: ignore[attr-defined]
-        return True
-
-
-class JSONFormatter(logging.Formatter):
-    """Emit log records as single-line JSON."""
-
-    def format(self, record: logging.LogRecord) -> str:
-        log_obj: dict = {
-            "timestamp": self.formatTime(record),
-            "level": record.levelname,
-            "logger": record.name,
-            "message": record.getMessage(),
-            "correlation_id": getattr(record, "correlation_id", None),
-        }
-        # Optional extra fields
-        for key in ("instance_id", "event_type"):
-            value = getattr(record, key, None)
-            if value is not None:
-                log_obj[key] = value
-        if record.exc_info:
-            log_obj["exception"] = self.formatException(record.exc_info)
-        return json.dumps(log_obj, default=str)
-
-    def formatTime(self, record: logging.LogRecord, datefmt: str | None = None) -> str:
-        return time.strftime("%Y-%m-%dT%H:%M:%S", time.gmtime(record.created))
-
-
 class RequestLoggingMiddleware(BaseHTTPMiddleware):
     """Log all HTTP requests with timing and status codes."""
 
@@ -54,6 +17,7 @@ class RequestLoggingMiddleware(BaseHTTPMiddleware):
         start_time = time.time()
         client_host = request.client.host if request.client else "unknown"
 
+        # Log the incoming request
         logger.info(
             "→ Request: %s %s (client: %s)",
             request.method,
@@ -65,6 +29,7 @@ class RequestLoggingMiddleware(BaseHTTPMiddleware):
             response = await call_next(request)
             duration = time.time() - start_time
 
+            # Log the response
             logger.info(
                 "← Response: %s %s → %d (%dms)",
                 request.method,
@@ -104,13 +69,15 @@ class ExceptionLoggingMiddleware(BaseHTTPMiddleware):
 
 
 def configure_logging(level: int = logging.INFO) -> None:
-    """Configure structured JSON logging for the application."""
+    """Configure structured logging for the application."""
-    formatter = JSONFormatter()
+    formatter = logging.Formatter(
+        fmt="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
 
     # Console handler
     console_handler = logging.StreamHandler(sys.stdout)
     console_handler.setFormatter(formatter)
-    console_handler.addFilter(CorrelationIdFilter())
 
     # Configure root logger
     root_logger = logging.getLogger()

apps/api/src/main.py

@@ -1,3 +1,4 @@
+import json
 import logging
 import os
 
@@ -6,36 +7,30 @@ from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
-
 from src.api.auth import router as auth_router
 from src.api.dashboard import router as dashboard_router
-from src.api.events import router as events_router
 from src.api.git_repositories import router as git_repositories_router
 from src.api.health import router as health_router
 from src.api.projects import router as projects_router
 from src.api.ssh_keys import router as ssh_keys_router
 from src.api.terminal import router as terminal_router
 from src.api.instance_proxy import router as instance_proxy_router
+from src.api.config_folders import router as config_folders_router
 from src.api.config_profiles import router as config_profiles_router
-from src.api.tool_definitions import router as tool_definitions_router
+from src.api.tool_configs import router as tool_configs_router
 from src.api.tool_instances import router as tool_instances_router
 from src.api.tool_instances import sessions_router
 from src.api.tool_types import router as tool_types_router
-from src.api.notifications import router as notifications_router
 from src.api.user_config import router as user_config_router
 from src.api.users import router as users_router
 from src.config import Settings
-from src.models.notification import Notification  # noqa: F401 – Alembic model discovery
+from src.database import SessionLocal, init_database
-from src.models.terminal_session import TerminalSessionModel  # noqa: F401 – Alembic model discovery
-from src.database import init_database
 from src.logging_config import (
     ExceptionLoggingMiddleware,
     RequestLoggingMiddleware,
     configure_logging,
 )
-from src.services.correlation import CorrelationIdMiddleware
+from src.seeds.builtin_tool_types import seed_builtin_tool_types
-from src.services.event_bus import InstanceEventBus
-from src.services.health_monitor import HealthMonitor
 
 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -60,7 +55,6 @@ app.add_middleware(
     allow_headers=["*"],
 )
 
-app.add_middleware(CorrelationIdMiddleware)
 app.add_middleware(RequestLoggingMiddleware)
 app.add_middleware(ExceptionLoggingMiddleware)
 
@@ -73,9 +67,7 @@ def _sanitize_validation_errors(errors):
             "type": error.get("type"),
             "loc": error.get("loc"),
             "msg": error.get("msg"),
-            "input": str(error.get("input"))
+            "input": str(error.get("input")) if error.get("input") is not None else None,
-            if error.get("input") is not None
-            else None,
         }
         # Convert ctx to safe format
         ctx = error.get("ctx")
@@ -110,11 +102,6 @@ async def validation_exception_handler(request: Request, exc: RequestValidationE
     )
 
 
-# Global services
-_event_bus = InstanceEventBus()
-_health_monitor = HealthMonitor(_event_bus)
-
-
 @app.on_event("startup")
 async def on_startup():
     logger.info("Starting up Headquarter API...")
@@ -124,24 +111,12 @@ async def on_startup():
     if not db_ready:
         logger.error("Database initialization failed. Shutting down.")
         import sys
-
         sys.exit(1)
 
-    # Start background health monitor
+    # Seed built-in data
-    _health_monitor.start()
+    await seed_builtin_tool_types()
-    logger.info("Health monitor started")
-
     logger.info("Startup complete.")
 
-
-@app.on_event("shutdown")
-async def on_shutdown():
-    logger.info("Shutting down Headquarter API...")
-    _health_monitor.stop()
-    logger.info("Health monitor stopped")
-    logger.info("Shutdown complete.")
-
-
 app.include_router(health_router)
 app.include_router(auth_router)
 app.include_router(dashboard_router)
@@ -151,12 +126,11 @@ app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
-app.include_router(tool_definitions_router)
+app.include_router(config_folders_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
+app.include_router(tool_configs_router)
 app.include_router(sessions_router)
 app.include_router(instance_proxy_router)
 app.include_router(terminal_router)
-app.include_router(events_router)
-app.include_router(notifications_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")

apps/api/src/models/__init__.py

@@ -1,13 +1,11 @@
 from src.models.base import Base
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.config_folder import ConfigFolder
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
 from src.models.git_repository import GitRepository
-from src.models.health_check import HealthCheck
-from src.models.instance_event import InstanceEvent
-from src.models.notification import Notification
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
-from src.models.terminal_session import TerminalSessionModel
-from src.models.tool_definition_manifest import ToolDefinitionManifest
 from src.models.tool_instance import ToolInstance
 from src.models.tool_type import ToolType
 from src.models.user import User
@@ -15,16 +13,13 @@ from src.models.user_config import UserConfig
 
 __all__ = [
     "Base",
+    "ConfigFolder",
+    "ConfigInclude",
+    "ConfigMount",
     "ConfigProfile",
-    "ConfigProfileInclude",
     "GitRepository",
-    "HealthCheck",
-    "InstanceEvent",
-    "Notification",
     "Project",
     "SSHKey",
-    "TerminalSessionModel",
-    "ToolDefinitionManifest",
     "ToolInstance",
     "ToolType",
     "User",

apps/api/src/models/config_folder.py

@@ -0,0 +1,33 @@
+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 ConfigFolder(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_folders"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
+    )
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    mount_path: Mapped[str] = mapped_column(String(1024), nullable=False)
+    files: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"relative/path": "content", ...}
+    project_overrides: Mapped[dict | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )  # {"project_id": {"mount_path": "...", "files": {...}}}
+    # DEPRECATED: Legacy auto-mounting flag. No longer used for launch-time
+    # auto-mounting. Use ConfigProfile and ToolInstance.selected_profile_id instead.
+    is_active: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
+
+    user: Mapped["User"] = relationship()

apps/api/src/models/config_include.py

@@ -0,0 +1,36 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, Integer, UniqueConstraint
+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.config_profile import ConfigProfile
+
+
+class ConfigInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_includes"
+    __table_args__ = (
+        UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
+    )
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    included_profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="includes",
+    )
+    included_profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[included_profile_id],
+    )

apps/api/src/models/config_mount.py

@@ -0,0 +1,31 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, Integer, JSON, String
+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.config_profile import ConfigProfile
+
+
+class ConfigMount(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_mounts"
+
+    profile_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
+    )
+    target_path: Mapped[str] = mapped_column(String(1024), nullable=False)
+    mode: Mapped[str] = mapped_column(String(10), nullable=False, default="rw")
+    files: Mapped[dict[str, str] | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
+
+    profile: Mapped["ConfigProfile"] = relationship(
+        "ConfigProfile",
+        foreign_keys=[profile_id],
+        back_populates="mounts",
+    )

apps/api/src/models/config_profile.py

@@ -1,13 +1,15 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import ForeignKey, JSON, Integer, String, Text, Boolean
+from sqlalchemy import ForeignKey, Integer, JSON, String, Text, UniqueConstraint
 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.config_include import ConfigInclude
+    from src.models.config_mount import ConfigMount
     from src.models.project import Project
     from src.models.tool_type import ToolType
     from src.models.user import User
@@ -15,63 +17,43 @@ if TYPE_CHECKING:
 
 class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     __tablename__ = "config_profiles"
+    __table_args__ = (
+        UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
 
     user_id: Mapped[uuid.UUID] = mapped_column(
         UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
     )
-    name: Mapped[str] = mapped_column(String(255), nullable=False)
-    description: Mapped[str | None] = mapped_column(Text, nullable=True)
     project_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("projects.id", ondelete="CASCADE"), nullable=True
     )
     tool_type_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True
     )
-    env_vars: Mapped[dict] = mapped_column(
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
-        JSON, default=dict, nullable=False
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    )  # {"VAR_NAME": "value", ...}
+    environment_variables: Mapped[dict[str, str] | None] = mapped_column(
-    runtime_hints: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=True
-        JSON, default=dict, nullable=False
+    )
-    )  # {"start_command": "...", "working_dir": "...", ...}
+    start_command: Mapped[str | None] = mapped_column(Text, nullable=True)
-    mounts: Mapped[list] = mapped_column(
+    working_directory: Mapped[str | None] = mapped_column(Text, nullable=True)
-        JSON, default=list, nullable=False
+    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
-    )  # [{"target": "/path", "mode": "rw", "files": {"rel/path": "content"}}, ...]
+    is_default: Mapped[bool] = mapped_column(default=False, nullable=False)
-    files: Mapped[dict] = mapped_column(
-        JSON, default=dict, nullable=False
-    )  # {"rel/path": "content", ...}
-    git_mounts: Mapped[list] = mapped_column(
-        JSON, default=list, nullable=False
-    )  # [{"remote_url": "https://github.com/user/repo.git", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
-    is_default: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
 
     user: Mapped["User"] = relationship()
     project: Mapped["Project | None"] = relationship()
     tool_type: Mapped["ToolType | None"] = relationship()
-    includes: Mapped[list["ConfigProfileInclude"]] = relationship(
+    includes: Mapped[list["ConfigInclude"]] = relationship(
-        "ConfigProfileInclude",
+        "ConfigInclude",
-        foreign_keys="ConfigProfileInclude.profile_id",
+        primaryjoin="ConfigProfile.id == ConfigInclude.profile_id",
-        order_by="ConfigProfileInclude.order_index",
+        back_populates="profile",
         cascade="all, delete-orphan",
+        order_by="ConfigInclude.order_index",
     )
-
+    mounts: Mapped[list["ConfigMount"]] = relationship(
-
+        "ConfigMount",
-class ConfigProfileInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+        primaryjoin="ConfigProfile.id == ConfigMount.profile_id",
-    __tablename__ = "config_profile_includes"
+        back_populates="profile",
-
+        cascade="all, delete-orphan",
-    profile_id: Mapped[uuid.UUID] = mapped_column(
+        order_by="ConfigMount.order_index",
-        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
-    )
-    included_profile_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False
-    )
-    order_index: Mapped[int] = mapped_column(Integer, nullable=False, default=0)
-
-    profile: Mapped["ConfigProfile"] = relationship(
-        "ConfigProfile",
-        foreign_keys=[profile_id],
-        back_populates="includes",
-    )
-    included_profile: Mapped["ConfigProfile"] = relationship(
-        "ConfigProfile",
-        foreign_keys=[included_profile_id],
     )

apps/api/src/models/git_repository.py

@@ -10,7 +10,6 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.ssh_key import SSHKey
     from src.models.user import User
 
 
@@ -19,15 +18,11 @@ class GitRepository(UUIDPrimaryKeyMixin, TimestampMixin, Base):
 
     name: Mapped[str] = mapped_column(String(255))
     path: Mapped[str] = mapped_column(String(1024))
-    project_id: Mapped[uuid.UUID | None] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=True)
+    project_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=False)
     owner_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False)
     is_mirror: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
     remote_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
     last_push: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
-    ssh_key_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(), ForeignKey("ssh_keys.id"), nullable=True
-    )
 
     project: Mapped["Project"] = relationship(back_populates="repositories")
     owner: Mapped["User"] = relationship()
-    ssh_key: Mapped["SSHKey | None"] = relationship()

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_config.py

@@ -0,0 +1,48 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import 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.project import Project
+    from src.models.tool_type import ToolType
+    from src.models.user import User
+
+
+class ToolConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "tool_configs"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id"), nullable=False
+    )
+    tool_type_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("tool_types.id"), nullable=False
+    )
+    project_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("projects.id"), nullable=True
+    )
+    key: Mapped[str] = mapped_column(String(255), nullable=False)
+    value: Mapped[str] = mapped_column(Text, nullable=False)
+    config_type: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="env"
+    )  # "env" or "file"
+    file_path: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )  # Only for file type
+    port_override: Mapped[int | None] = mapped_column(nullable=True)
+    start_command: Mapped[str | None] = mapped_column(Text, nullable=True)
+    working_directory: Mapped[str | None] = mapped_column(Text, nullable=True)
+    environment_variables: Mapped[dict | None] = mapped_column(
+        JSON, default=dict, nullable=True
+    )
+    volumes: Mapped[list[dict] | None] = mapped_column(
+        JSON, default=list, nullable=True
+    )
+
+    user: Mapped["User"] = relationship()
+    tool_type: Mapped["ToolType"] = relationship()
+    project: Mapped["Project | None"] = relationship()

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/tool_instance.py

@@ -2,7 +2,7 @@ import uuid
 from datetime import datetime
 from typing import TYPE_CHECKING
 
-from sqlalchemy import DateTime, ForeignKey, Integer, JSON, String
+from sqlalchemy import DateTime, ForeignKey, Integer, String
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
@@ -33,36 +33,42 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     owner_id: Mapped[uuid.UUID] = mapped_column(
         UUID(), ForeignKey("users.id"), nullable=False
     )
-    status: Mapped[str] = mapped_column(String(50), nullable=False, default="pending")
+    status: Mapped[str] = mapped_column(
-    container_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+        String(50), nullable=False, default="pending"
-    container_name: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    )
-    compose_path: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    container_id: Mapped[str | None] = mapped_column(
-    url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+        String(255), nullable=True
-    public_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    )
-    tunnel_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    container_name: Mapped[str | None] = mapped_column(
-    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
+        String(255), nullable=True
+    )
+    compose_path: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    url: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    public_url: Mapped[str | None] = mapped_column(
+        String(1024), nullable=True
+    )
+    tunnel_id: Mapped[str | None] = mapped_column(
+        String(255), nullable=True
+    )
+    port: Mapped[int | None] = mapped_column(
+        Integer, nullable=True
+    )
     last_started_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
     last_stopped_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
-    manifest_compiled_at: Mapped[datetime | None] = mapped_column(
+    selected_profile_id: Mapped[uuid.UUID | None] = mapped_column(
-        DateTime(timezone=True), nullable=True
-    )
-    image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
-    probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
-    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
-    branch: Mapped[str | None] = mapped_column(
-        String(255), nullable=True, default="main"
-    )
-    selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
     )
-    ssh_key_ids: Mapped[list[str] | None] = mapped_column(JSON, nullable=True)
 
     tool_type: Mapped["ToolType"] = relationship()
     repository: Mapped["GitRepository"] = relationship()
     project: Mapped["Project"] = relationship()
     owner: Mapped["User"] = relationship()
-    selected_config_profile: Mapped["ConfigProfile | None"] = relationship()
+    selected_profile: Mapped["ConfigProfile | None"] = relationship()

apps/api/src/models/tool_type.py

@@ -8,7 +8,6 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
-    from src.models.tool_definition_manifest import ToolDefinitionManifest
     from src.models.user import User
 
 
@@ -19,36 +18,23 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     display_name: Mapped[str] = mapped_column(String(255), nullable=False)
     description: Mapped[str | None] = mapped_column(Text, nullable=True)
     category: Mapped[str] = mapped_column(String(50), nullable=False, default="other")
-    interface_type: Mapped[str] = mapped_column(
+    interfaces: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
-        String(20), nullable=False, default="web"
-    )
-    requires_port: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
     default_port: Mapped[int] = mapped_column(nullable=False)
     definition_type: Mapped[str] = mapped_column(
-        String(16), nullable=False, default="legacy"
+        String(20), nullable=False, default="compose"
-    )  # "legacy" | "manifest"
+    )  # "compose" or "dockerfile"
-    manifest_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(),
-        ForeignKey("tool_definition_manifests.id"),
-        nullable=True,
-    )
     compose_template: Mapped[str | None] = mapped_column(Text, nullable=True)
     dockerfile_template: Mapped[str | None] = mapped_column(Text, nullable=True)
     build_context: Mapped[dict | None] = mapped_column(
         JSON, default=dict, nullable=True
     )
     readiness_probe: Mapped[dict | None] = mapped_column(JSON, nullable=True)
-    startup_command: Mapped[str | None] = mapped_column(Text, nullable=True)
+    required_variables: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
-    required_variables: Mapped[list[str]] = mapped_column(
+    is_builtin: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
-        JSON, default=list, nullable=False
-    )
     created_by_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(),
         ForeignKey("users.id"),
         nullable=True,
     )
 
-    manifest: Mapped["ToolDefinitionManifest | None"] = relationship(
-        foreign_keys=[manifest_id],
-    )
     created_by: Mapped["User | None"] = relationship()

apps/api/src/models/user_config.py

@@ -18,3 +18,23 @@ class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     config: Mapped[dict[str, object]] = mapped_column(JSON, default=dict, nullable=False)
 
     user: Mapped["User"] = relationship(back_populates="user_config")
+
+    @property
+    def default_profile_id(self) -> uuid.UUID | None:
+        profile_id = self.config.get("default_profile_id")
+        return uuid.UUID(profile_id) if profile_id else None
+
+    @default_profile_id.setter
+    def default_profile_id(self, value: uuid.UUID | None) -> None:
+        if value is not None:
+            self.config["default_profile_id"] = str(value)
+        elif "default_profile_id" in self.config:
+            del self.config["default_profile_id"]
+
+    @property
+    def default_profiles(self) -> dict[str, str]:
+        return self.config.get("default_profiles", {})
+
+    @default_profiles.setter
+    def default_profiles(self, value: dict[str, str]) -> None:
+        self.config["default_profiles"] = value

apps/api/src/schemas/__init__.py

@@ -0,0 +1 @@
+"""Pydantic request/response schemas."""

apps/api/src/schemas/config_folder.py

@@ -0,0 +1,44 @@
+"""Config folder request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, Field
+
+
+class ConfigFolderCreate(BaseModel):
+    name: str = Field(description="Folder name")
+    description: str | None = Field(default=None, description="Optional description")
+    mount_path: str = Field(description="Mount path in container")
+    files: dict[str, str] | None = Field(
+        default=None, description="Files as {path: content}"
+    )
+    is_active: bool = Field(default=True, description="Whether folder is active")
+
+
+class ConfigFolderUpdate(BaseModel):
+    name: str | None = None
+    description: str | None = None
+    mount_path: str | None = None
+    files: dict[str, str] | None = None
+    is_active: bool | None = None
+
+
+class ProjectOverrideCreate(BaseModel):
+    project_id: str = Field(description="Project ID to override for")
+    mount_path: str | None = Field(default=None, description="Override mount path")
+    files: dict[str, str] | None = Field(
+        default=None, description="Override files"
+    )
+    is_active: bool | None = Field(default=None, description="Override active state")
+
+
+class ConfigFolderResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    mount_path: str
+    files: dict[str, str] | None
+    is_active: bool
+    created_at: str
+    updated_at: str

apps/api/src/schemas/config_profile.py

@@ -0,0 +1,131 @@
+"""Config profile request/response schemas."""
+
+from typing import Any
+
+from pydantic import BaseModel, Field, field_validator
+
+MAX_MOUNT_PATH_LENGTH = 1024
+
+
+class ConfigProfileCreate(BaseModel):
+    name: str = Field(description="Profile name (unique per user)")
+    description: str | None = Field(default=None, description="Optional description")
+
+    @field_validator("name")
+    @classmethod
+    def validate_name(cls, v: str) -> str:
+        v = v.strip()
+        if not v:
+            raise ValueError("Profile name cannot be empty")
+        if len(v) > 255:
+            raise ValueError("Profile name must be 255 characters or less")
+        return v
+
+
+class ConfigProfileUpdate(BaseModel):
+    name: str | None = Field(default=None, description="Profile name")
+    description: str | None = Field(default=None, description="Optional description")
+
+    @field_validator("name")
+    @classmethod
+    def validate_name(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        v = v.strip()
+        if not v:
+            raise ValueError("Profile name cannot be empty")
+        if len(v) > 255:
+            raise ValueError("Profile name must be 255 characters or less")
+        return v
+
+
+class ConfigProfileResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    created_at: str
+    updated_at: str
+
+
+class ConfigProfileDetailResponse(ConfigProfileResponse):
+    includes: list[dict[str, Any]]
+    mounts: list[dict[str, Any]]
+
+
+class ConfigIncludeCreate(BaseModel):
+    included_profile_id: str = Field(description="UUID of the profile to include")
+    order_index: int = Field(default=0, description="Order index for include resolution")
+
+
+class ConfigIncludeUpdate(BaseModel):
+    order_index: int = Field(description="Order index for include resolution")
+
+
+class ConfigIncludeResponse(BaseModel):
+    id: str
+    profile_id: str
+    included_profile_id: str
+    included_profile_name: str | None
+    order_index: int
+    created_at: str
+    updated_at: str
+
+
+class ConfigMountCreate(BaseModel):
+    target_path: str = Field(description="Absolute target path in container")
+    mode: str = Field(default="rw", description="Mount mode (rw or ro)")
+    files: dict[str, str] | None = Field(
+        default=None, description="Files as {path: content}"
+    )
+    order_index: int = Field(default=0, description="Order index for mount resolution")
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str) -> str:
+        if not v.startswith("/"):
+            raise ValueError("Target path must be absolute (start with /)")
+        if ".." in v:
+            raise ValueError("Target path cannot contain parent directory references (..)")
+        if len(v) > MAX_MOUNT_PATH_LENGTH:
+            raise ValueError(f"Target path must be {MAX_MOUNT_PATH_LENGTH} characters or less")
+        return v
+
+
+class ConfigMountUpdate(BaseModel):
+    target_path: str | None = Field(default=None, description="Absolute target path in container")
+    mode: str | None = Field(default=None, description="Mount mode (rw or ro)")
+    files: dict[str, str] | None = Field(
+        default=None, description="Files as {path: content}"
+    )
+    order_index: int | None = Field(default=None, description="Order index for mount resolution")
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if not v.startswith("/"):
+            raise ValueError("Target path must be absolute (start with /)")
+        if ".." in v:
+            raise ValueError("Target path cannot contain parent directory references (..)")
+        if len(v) > MAX_MOUNT_PATH_LENGTH:
+            raise ValueError(f"Target path must be {MAX_MOUNT_PATH_LENGTH} characters or less")
+        return v
+
+
+class ConfigMountResponse(BaseModel):
+    id: str
+    profile_id: str
+    target_path: str
+    mode: str
+    files: dict[str, str] | None
+    order_index: int
+    created_at: str
+    updated_at: str
+
+
+class DefaultProfilesUpdate(BaseModel):
+    default_profiles: dict[str, str] = Field(
+        description="Mapping of tool_type_id to profile_id"
+    )

apps/api/src/schemas/git_repository.py

@@ -0,0 +1,129 @@
+"""Git repository request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict
+
+
+class GitRepositoryCreate(BaseModel):
+    name: str
+    remote_url: str | None = None
+    force_original_url: bool = False
+
+
+class URLParseRequest(BaseModel):
+    url: str
+
+
+class URLParseResponse(BaseModel):
+    original_url: str
+    base_url: str | None
+    is_valid_clone_url: bool
+    needs_parsing: bool
+    host: str | None
+    message: str
+    error_code: str | None
+
+
+class GitRepositoryResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    path: str
+    project_id: uuid.UUID
+    owner_id: uuid.UUID
+    is_mirror: bool
+    remote_url: str | None
+    last_push: datetime | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class FileListResponse(BaseModel):
+    path: str
+    branch: str
+    entries: list[dict]
+
+
+class FileContentResponse(BaseModel):
+    path: str
+    branch: str
+    content: str
+    size: int
+    encoding: str
+    language: str | None
+    is_binary: bool
+    last_commit: dict | None
+
+
+class BranchesResponse(BaseModel):
+    branches: list[dict]
+    default_branch: str
+
+
+class FileUpdateRequest(BaseModel):
+    path: str
+    branch: str
+    content: str
+    commit_message: str
+
+
+class FileUpdateResponse(BaseModel):
+    commit_hash: str
+    message: str
+    branch: str
+
+
+class StatusResponse(BaseModel):
+    branch: str
+    modified: list[str]
+    added: list[str]
+    deleted: list[str]
+    untracked: list[str]
+    renamed: list[str]
+    ahead: int
+    behind: int
+
+
+class BranchCreateRequest(BaseModel):
+    name: str
+    base_branch: str = "HEAD"
+
+
+class CheckoutRequest(BaseModel):
+    branch: str
+
+
+class CommitRequest(BaseModel):
+    message: str
+    files: list[str] | None = None
+
+
+class CommitResponse(BaseModel):
+    commit_hash: str
+    message: str
+
+
+class FetchResponse(BaseModel):
+    message: str
+
+
+class PullResponse(BaseModel):
+    message: str
+
+
+class PushResponse(BaseModel):
+    message: str
+
+
+class MergeRequest(BaseModel):
+    source_branch: str
+    target_branch: str | None = None
+    message: str | None = None
+
+
+class MergeResponse(BaseModel):
+    commit_hash: str
+    message: str

apps/api/src/schemas/health.py

@@ -0,0 +1,50 @@
+"""Health check response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class DatabaseHealth(BaseModel):
+    """Database health check result."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(
+        description="Query response time in milliseconds", examples=[5.2]
+    )
+
+
+class DiskHealth(BaseModel):
+    """Disk space health check result."""
+
+    status: str = Field(description="Disk health status", examples=["healthy"])
+    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
+    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
+
+
+class HealthChecks(BaseModel):
+    """Individual health checks."""
+
+    database: DatabaseHealth | None = None
+    disk: DiskHealth | None = None
+
+
+class HealthResponse(BaseModel):
+    """Overall health check response."""
+
+    status: str = Field(description="Overall health status", examples=["healthy"])
+    timestamp: str = Field(
+        description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"]
+    )
+    version: str = Field(description="API version", examples=["0.1.0"])
+    checks: HealthChecks = Field(description="Individual health checks")
+    uptime_seconds: float = Field(
+        description="Server uptime in seconds", examples=[3600.0]
+    )
+
+
+class DatabaseHealthResponse(BaseModel):
+    """Database-specific health check response."""
+
+    status: str = Field(description="Database health status", examples=["healthy"])
+    response_time_ms: float = Field(
+        description="Query response time in milliseconds", examples=[5.2]
+    )

apps/api/src/schemas/project.py

@@ -0,0 +1,25 @@
+"""Project request/response schemas."""
+
+from pydantic import BaseModel
+
+
+class ProjectCreate(BaseModel):
+    name: str
+    description: str | None = None
+
+
+class ProjectUpdate(BaseModel):
+    name: str | None = None
+    description: str | None = None
+
+
+class ProjectResponse(BaseModel):
+    id: str
+    name: str
+    description: str | None
+    created_at: str
+    updated_at: str
+
+
+class SetDefaultSSHKeyRequest(BaseModel):
+    ssh_key_id: str

apps/api/src/schemas/ssh_key.py

@@ -0,0 +1,16 @@
+"""SSH key request/response schemas."""
+
+from pydantic import BaseModel
+
+
+class SSHKeyCreate(BaseModel):
+    name: str
+    public_key: str
+
+
+class SSHKeyResponse(BaseModel):
+    id: str
+    name: str
+    public_key: str
+    fingerprint: str
+    created_at: str

apps/api/src/schemas/tool_config.py

@@ -0,0 +1,47 @@
+"""Tool config request/response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class ToolConfigCreate(BaseModel):
+    tool_type_id: str = Field(description="UUID of the tool type")
+    key: str = Field(description="Configuration key")
+    value: str = Field(description="Configuration value")
+    config_type: str = Field(default="env", description="Config type: env or file")
+    file_path: str | None = Field(default=None, description="File path for file configs")
+    port_override: int | None = Field(default=None, description="Port override")
+    start_command: str | None = Field(default=None, description="Start command override")
+    working_directory: str | None = Field(default=None, description="Working directory")
+    environment_variables: dict[str, str] | None = Field(
+        default=None, description="Additional environment variables"
+    )
+    volumes: list[dict] | None = Field(default=None, description="Volume mounts")
+
+
+class ToolConfigUpdate(BaseModel):
+    value: str | None = None
+    config_type: str | None = None
+    file_path: str | None = None
+    port_override: int | None = None
+    start_command: str | None = None
+    working_directory: str | None = None
+    environment_variables: dict[str, str] | None = None
+    volumes: list[dict] | None = None
+
+
+class ToolConfigResponse(BaseModel):
+    id: str
+    tool_type_id: str
+    user_id: str
+    project_id: str | None
+    key: str
+    value: str
+    config_type: str
+    file_path: str | None
+    port_override: int | None
+    start_command: str | None
+    working_directory: str | None
+    environment_variables: dict[str, str] | None
+    volumes: list[dict] | None
+    created_at: str
+    updated_at: str

apps/api/src/schemas/tool_instance.py

@@ -0,0 +1,41 @@
+"""Tool instance request/response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class CreateInstanceRequest(BaseModel):
+    """Request body for creating a tool instance."""
+
+    model_config = {"extra": "ignore"}
+
+    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
+    display_name: str | None = Field(
+        default=None, description="Optional display name for the instance"
+    )
+    config_profile_id: str | None = Field(
+        default=None, description="Optional config profile ID to apply to the instance"
+    )
+
+
+class SessionItemResponse(BaseModel):
+    """Lightweight session summary for sidebar and dashboard."""
+
+    model_config = {"extra": "ignore"}
+
+    id: str = Field(description="Session (tool instance) ID")
+    display_name: str = Field(description="Display name of the session")
+    tool_type_name: str = Field(description="Name of the tool type")
+    tool_icon: str | None = Field(default=None, description="Icon URL for the tool type")
+    tool_type_interfaces: list[str] = Field(default_factory=list, description="Supported interfaces")
+    repository_name: str = Field(description="Name of the repository")
+    repository_id: str = Field(description="Repository ID")
+    project_name: str = Field(description="Name of the project")
+    project_id: str = Field(description="Project ID")
+    status: str = Field(description="Current status")
+    url: str | None = Field(default=None, description="Access URL")
+
+
+class SessionListResponse(BaseModel):
+    """Response wrapping a list of session summaries."""
+
+    sessions: list[SessionItemResponse]

apps/api/src/schemas/tool_type.py

@@ -0,0 +1,204 @@
+"""Tool type request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+import yaml
+from pydantic import BaseModel, ConfigDict, field_validator, model_validator
+
+
+class ToolTypeCreate(BaseModel):
+    name: str
+    display_name: str
+    description: str | None = None
+    default_port: int
+    definition_type: str = "compose"
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    required_variables: list[str] = []
+    category: str = "other"
+    interfaces: list[str] = ["web"]
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str) -> str:
+        if v not in ("compose", "dockerfile"):
+            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+        if v is None:
+            raise ValueError("compose_template is required when definition_type is 'compose'")
+        try:
+            parsed = yaml.safe_load(v)
+        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 v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "dockerfile":
+            return v
+        if v is None:
+            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        return v
+
+    @field_validator("default_port")
+    @classmethod
+    def validate_default_port(cls, v: int, info) -> int:
+        if v <= 0 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+        template = data.get("compose_template")
+        if not template:
+            return v
+        try:
+            parsed = yaml.safe_load(template)
+        except yaml.YAMLError:
+            return v
+        port_str = str(v)
+        port_exposed = False
+        if isinstance(parsed, dict) and "services" in parsed:
+            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:
+                            port_exposed = True
+                            break
+                        elif isinstance(port_mapping, int) and port_mapping == v:
+                            port_exposed = True
+                            break
+                if port_exposed:
+                    break
+        if not port_exposed:
+            raise ValueError(f"Port {v} is not exposed in the compose template. Add it to the 'ports' section.")
+        return v
+
+    @field_validator("required_variables")
+    @classmethod
+    def validate_required_variables(cls, v: list[str], info) -> list[str]:
+        if not v:
+            return v
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+        template = data.get("compose_template")
+        if not template:
+            return v
+        for var in v:
+            placeholder = f"{{{{{var}}}}}"
+            if placeholder not in template:
+                raise ValueError(f"Required variable '{var}' not found in compose template")
+        return v
+
+    @model_validator(mode="after")
+    def validate_templates(self) -> "ToolTypeCreate":
+        if self.definition_type == "dockerfile" and self.dockerfile_template is None:
+            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
+        if self.definition_type == "compose" and self.compose_template is None:
+            raise ValueError("compose_template is required when definition_type is 'compose'")
+        return self
+
+
+class ToolTypeUpdate(BaseModel):
+    display_name: str | None = None
+    description: str | None = None
+    default_port: int | None = None
+    definition_type: str | None = None
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    required_variables: list[str] | None = None
+    category: str | None = None
+    interfaces: list[str] | None = None
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("compose", "dockerfile"):
+            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        data = info.data
+        definition_type = data.get("definition_type")
+        if definition_type and definition_type != "compose":
+            return v
+        try:
+            parsed = yaml.safe_load(v)
+        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 v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        data = info.data
+        definition_type = data.get("definition_type")
+        if definition_type and definition_type != "dockerfile":
+            return v
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        return v
+
+
+class ToolTypeResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    display_name: str
+    description: str | None
+    category: str
+    interfaces: list[str]
+    default_port: int
+    definition_type: str
+    compose_template: str | None
+    dockerfile_template: str | None
+    build_context: dict | None
+    readiness_probe: dict | None
+    required_variables: list[str]
+    is_builtin: bool
+    created_by_id: uuid.UUID | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class ToolTypeValidateRequest(BaseModel):
+    definition_type: str
+    compose_template: str | None = None
+    dockerfile_template: str | None = None

apps/api/src/schemas/user.py

@@ -0,0 +1,19 @@
+"""User request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserProfileResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    email: str
+    name: str
+    avatar_url: str | None
+
+
+class UserProfileUpdate(BaseModel):
+    name: str | None = None
+    email: str | None = None

apps/api/src/schemas/user_config.py

@@ -0,0 +1,21 @@
+"""User config request/response schemas."""
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserConfigResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    default_editor: str | None = None
+    theme: str = "system"
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None
+
+
+class UserConfigUpdate(BaseModel):
+    default_editor: str | None = None
+    theme: str | None = None
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None

apps/api/src/seeds/builtin_tool_types.py

@@ -0,0 +1,161 @@
+import logging
+
+from sqlalchemy import select
+
+from src.database import SessionLocal
+from src.models.tool_type import ToolType
+
+logger = logging.getLogger(__name__)
+
+
+async def _table_exists(session, table_name: str) -> bool:
+    """Check if a table exists in the database."""
+    from sqlalchemy import text
+
+    try:
+        result = await session.execute(
+            text(
+                """
+                SELECT EXISTS (
+                    SELECT FROM information_schema.tables
+                    WHERE table_schema = 'public'
+                    AND table_name = :table_name
+                )
+            """
+            ),
+            {"table_name": table_name},
+        )
+        return result.scalar() or False
+    except Exception:
+        return False
+
+
+async def seed_builtin_tool_types():
+    async with SessionLocal() as session:
+        # Check if tool_types table exists before attempting to seed
+        if not await _table_exists(session, "tool_types"):
+            logger.warning(
+                "tool_types table does not exist. Skipping seeding. "
+                "Migrations may not have run yet."
+            )
+            return
+
+        builtin_types = [
+            {
+                "name": "code-server",
+                "display_name": "VS Code Server",
+                "description": "VS Code running in the browser via code-server",
+                "category": "editor",
+                "interfaces": ["web"],
+                "compose_template": """version: "3.8"
+services:
+  code-server:
+    image: lscr.io/linuxserver/code-server:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - PUID=1000
+      - PGID=1000
+      - TZ=Europe/London
+    volumes:
+      - {{REPO_PATH}}:/config/workspace
+    ports:
+      - "8443:8443"
+    restart: unless-stopped""",
+                "default_port": 8443,
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "jupyter-notebook",
+                "display_name": "Jupyter Notebook",
+                "description": "Jupyter Lab for interactive development",
+                "category": "notebook",
+                "interfaces": ["web"],
+                "default_port": 8888,
+                "compose_template": """version: "3.8"
+services:
+  jupyter:
+    image: jupyter/scipy-notebook:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - JUPYTER_ENABLE_LAB=yes
+    volumes:
+      - {{REPO_PATH}}:/home/jovyan/work
+    ports:
+      - "8888:8888"
+    restart: unless-stopped""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "opencode",
+                "display_name": "OpenCode",
+                "description": "AI coding assistant - run opencode in terminal",
+                "category": "ai-assistant",
+                "interfaces": ["terminal"],
+                "default_port": 3000,
+                "compose_template": """version: "3.8"
+services:
+  opencode:
+    image: node:20-slim
+    container_name: {{TOOL_NAME}}
+    working_dir: /workspace
+    environment:
+      - HOME=/tmp
+    volumes:
+      - {{REPO_PATH}}:/workspace
+      - opencode_home:/tmp
+    ports:
+      - "3000:3000"
+    command: >
+      sh -c "set -x &&
+             apt-get update && apt-get install -y git ca-certificates &&
+             echo 'Installing opencode...' &&
+             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
+             which opencode || echo 'ERROR: opencode not in PATH' &&
+             npm bin -g &&
+             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
+             echo 'export PATH=\"$(npm bin -g):\\$PATH\"' >> /root/.bashrc &&
+             echo 'cd /workspace' >> /root/.bashrc &&
+             echo 'OpenCode installation complete' &&
+             cd /workspace &&
+             exec tail -f /dev/null"
+    stdin_open: true
+    tty: true
+    restart: unless-stopped
+
+volumes:
+  opencode_home:""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+        ]
+
+        for tool_data in builtin_types:
+            existing = await session.scalar(select(ToolType).where(ToolType.name == tool_data["name"]))
+            if not existing:
+                tool_type = ToolType(
+                    name=tool_data["name"],
+                    display_name=tool_data["display_name"],
+                    description=tool_data["description"],
+                    category=tool_data["category"],
+                    interfaces=tool_data["interfaces"],
+                    definition_type="compose",
+                    compose_template=tool_data["compose_template"],
+                    required_variables=tool_data["required_variables"],
+                    default_port=tool_data.get("default_port"),
+                    is_builtin=True,
+                )
+                session.add(tool_type)
+                logger.info("Created built-in tool type: %s", tool_data["name"])
+            else:
+                # Update existing built-in tool types to reflect code changes
+                existing.display_name = tool_data["display_name"]
+                existing.description = tool_data["description"]
+                existing.category = tool_data["category"]
+                existing.interfaces = tool_data["interfaces"]
+                existing.definition_type = "compose"
+                existing.compose_template = tool_data["compose_template"]
+                existing.required_variables = tool_data["required_variables"]
+                existing.default_port = tool_data.get("default_port")
+                logger.info("Updated built-in tool type: %s", tool_data["name"])
+
+        await session.commit()
+        logger.info("Built-in tool types seeded successfully.")

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/config_profiles.py

@@ -0,0 +1,299 @@
+"""Config profile business logic."""
+
+import logging
+import uuid
+
+from fastapi import HTTPException, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
+from src.models.tool_type import ToolType
+from src.models.user_config import UserConfig
+
+logger = logging.getLogger(__name__)
+
+MAX_INCLUDES_DEPTH = 10
+
+
+async def get_owned_profile(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID,
+    session: AsyncSession,
+) -> ConfigProfile:
+    """Fetch a config profile and verify ownership."""
+    profile = await session.get(ConfigProfile, profile_id)
+    if profile is None or profile.user_id != user_id:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail="config profile not found",
+        )
+    return profile
+
+
+async def _detect_cycle(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    visited: set[uuid.UUID] | None = None,
+    depth: int = 0,
+) -> bool:
+    """Detect cycles in profile includes using DFS.
+
+    Returns True if a cycle is detected.
+    """
+    if depth > MAX_INCLUDES_DEPTH:
+        return True
+
+    if visited is None:
+        visited = set()
+
+    if profile_id in visited:
+        return True
+
+    visited.add(profile_id)
+
+    result = await session.execute(
+        select(ConfigInclude.included_profile_id).where(
+            ConfigInclude.profile_id == profile_id
+        )
+    )
+    included_ids = result.scalars().all()
+
+    for included_id in included_ids:
+        if await _detect_cycle(session, included_id, visited.copy(), depth + 1):
+            return True
+
+    return False
+
+
+async def validate_includes_no_cycle(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    new_included_id: uuid.UUID | None = None,
+) -> None:
+    """Validate that adding an include wouldn't create a cycle."""
+    if new_included_id and await _detect_cycle(session, new_included_id, {profile_id}):
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="adding this include would create a circular reference",
+        )
+
+
+# ---------------------------------------------------------------------------
+# Profile CRUD helpers
+# ---------------------------------------------------------------------------
+
+async def check_duplicate_name(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    name: str,
+    exclude_id: uuid.UUID | None = None,
+) -> None:
+    """Raise 409 if a profile with the given name already exists."""
+    query = select(ConfigProfile).where(
+        ConfigProfile.user_id == user_id,
+        ConfigProfile.name == name,
+    )
+    if exclude_id:
+        query = query.where(ConfigProfile.id != exclude_id)
+    existing = await session.scalar(query)
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config profile with name '{name}' already exists",
+        )
+
+
+def profile_to_dict(profile: ConfigProfile) -> dict:
+    """Serialize a ConfigProfile to a dict."""
+    return {
+        "id": str(profile.id),
+        "user_id": str(profile.user_id),
+        "name": profile.name,
+        "description": profile.description,
+        "created_at": profile.created_at.isoformat() if profile.created_at else None,
+        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
+    }
+
+
+# ---------------------------------------------------------------------------
+# Include helpers
+# ---------------------------------------------------------------------------
+
+async def check_duplicate_include(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    included_profile_id: uuid.UUID,
+) -> None:
+    """Raise 409 if the include already exists."""
+    existing = await session.scalar(
+        select(ConfigInclude).where(
+            ConfigInclude.profile_id == profile_id,
+            ConfigInclude.included_profile_id == included_profile_id,
+        )
+    )
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="this include already exists",
+        )
+
+
+def include_to_dict(inc: ConfigInclude, included_name: str | None) -> dict:
+    """Serialize a ConfigInclude to a dict."""
+    return {
+        "id": str(inc.id),
+        "profile_id": str(inc.profile_id),
+        "included_profile_id": str(inc.included_profile_id),
+        "included_profile_name": included_name,
+        "order_index": inc.order_index,
+        "created_at": inc.created_at.isoformat() if inc.created_at else None,
+        "updated_at": inc.updated_at.isoformat() if inc.updated_at else None,
+    }
+
+
+# ---------------------------------------------------------------------------
+# Mount helpers
+# ---------------------------------------------------------------------------
+
+async def check_duplicate_mount_path(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+    target_path: str,
+    exclude_id: uuid.UUID | None = None,
+) -> None:
+    """Raise 409 if a mount with the given path already exists."""
+    query = select(ConfigMount).where(
+        ConfigMount.profile_id == profile_id,
+        ConfigMount.target_path == target_path,
+    )
+    if exclude_id:
+        query = query.where(ConfigMount.id != exclude_id)
+    existing = await session.scalar(query)
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"mount with path '{target_path}' already exists",
+        )
+
+
+def mount_to_dict(mount: ConfigMount) -> dict:
+    """Serialize a ConfigMount to a dict."""
+    return {
+        "id": str(mount.id),
+        "profile_id": str(mount.profile_id),
+        "target_path": mount.target_path,
+        "files": mount.files,
+        "mode": mount.mode,
+        "order_index": mount.order_index,
+        "created_at": mount.created_at.isoformat() if mount.created_at else None,
+        "updated_at": mount.updated_at.isoformat() if mount.updated_at else None,
+    }
+
+
+# ---------------------------------------------------------------------------
+# Default profile helpers
+# ---------------------------------------------------------------------------
+
+async def get_or_create_user_config(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+) -> UserConfig:
+    """Get existing user config or create a new one."""
+    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user_id))
+    user_config = result.scalar_one_or_none()
+    if user_config is None:
+        user_config = UserConfig(user_id=user_id, config={})
+        session.add(user_config)
+    return user_config
+
+
+async def validate_default_profiles(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    default_profiles: dict[str, str],
+) -> None:
+    """Validate that all profile IDs in default_profiles belong to the user."""
+    for tool_type_id, profile_id_str in default_profiles.items():
+        profile = await session.get(ConfigProfile, uuid.UUID(profile_id_str))
+        if profile is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=f"profile {profile_id_str} not found")
+        if profile.user_id != user_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail=f"profile {profile_id_str} does not belong to user")
+
+
+async def get_default_profiles(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+) -> dict:
+    """Get default profiles for a user."""
+    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user_id))
+    user_config = result.scalar_one_or_none()
+    return {"default_profiles": user_config.default_profiles if user_config else {}}
+
+
+async def set_default_profiles(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    default_profiles: dict[str, str],
+) -> dict:
+    """Set default profiles for a user."""
+    user_config = await get_or_create_user_config(session, user_id)
+    await validate_default_profiles(session, user_id, default_profiles)
+    user_config.config = {**user_config.config, "default_profiles": default_profiles}
+    await session.commit()
+    await session.refresh(user_config)
+    return {"default_profiles": user_config.default_profiles}
+
+
+async def get_default_profile_for_tool_type(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    tool_type_id: str,
+) -> dict:
+    """Get default profile for a specific tool type."""
+    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user_id))
+    user_config = result.scalar_one_or_none()
+    profile_id = user_config.default_profiles.get(tool_type_id) if user_config else None
+    return {"tool_type_id": tool_type_id, "profile_id": profile_id}
+
+
+# ---------------------------------------------------------------------------
+# Include list helper
+# ---------------------------------------------------------------------------
+
+async def list_includes_for_profile(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+) -> dict:
+    """List all includes for a profile."""
+    result = await session.execute(
+        select(ConfigInclude)
+        .where(ConfigInclude.profile_id == profile_id)
+        .order_by(ConfigInclude.order_index)
+    )
+    includes_data = []
+    for inc in result.scalars().all():
+        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
+        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
+    return {"includes": includes_data}
+
+
+# ---------------------------------------------------------------------------
+# Mount list helper
+# ---------------------------------------------------------------------------
+
+async def list_mounts_for_profile(
+    session: AsyncSession,
+    profile_id: uuid.UUID,
+) -> dict:
+    """List all mounts for a profile."""
+    result = await session.execute(
+        select(ConfigMount)
+        .where(ConfigMount.profile_id == profile_id)
+        .order_by(ConfigMount.order_index)
+    )
+    return {"mounts": [mount_to_dict(m) for m in result.scalars().all()]}

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

@@ -1,717 +0,0 @@
-"""Docker service for managing tool instances."""
-
-import logging
-import os
-import re
-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.
-
-    Searches all containers including stopped/exited ones.
-
-    Args:
-        instance_name: The service name in compose
-
-    Returns:
-        Container ID or None if not found
-    """
-    # Docker container names are lowercase internally; normalize to ensure match
-    result = subprocess.run(
-        ["docker", "ps", "-a", "-q", "--filter", f"name={instance_name.lower()}"],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
-    return None
-
-
-def get_container_name(instance_name: str) -> str | None:
-    """Get the full container name for a compose service.
-
-    Searches all containers including stopped/exited ones.
-
-    Args:
-        instance_name: The service name in compose
-
-    Returns:
-        Container name or None if not found
-    """
-    # Docker container names are lowercase internally; normalize to ensure match
-    result = subprocess.run(
-        [
-            "docker",
-            "ps",
-            "-a",
-            "--format",
-            "{{.Names}}",
-            "--filter",
-            f"name={instance_name.lower()}",
-        ],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
-    return None
-
-
-def connect_container_to_network(
-    container_name: str, network_name: str = "backend"
-) -> 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 (default: backend)
-
-    Returns:
-        True if successful, False otherwise
-    """
-    result = subprocess.run(
-        ["docker", "network", "connect", network_name, container_name],
-        capture_output=True,
-        text=True,
-    )
-    return result.returncode == 0
-
-
-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}")
-
-
-def _check_app_binding(container_name: str, port: int) -> dict[str, str | bool]:
-    """Diagnose whether the app is bound to 127.0.0.1 or 0.0.0.0.
-
-    Checks from both inside the container (localhost) and outside
-    (via Docker network) to detect binding issues.
-
-    Returns:
-        Dict with 'internal_ok', 'external_ok', 'internal_status',
-        'external_status', and 'diagnosis'.
-    """
-    import subprocess
-
-    result: dict[str, Any] = {
-        "internal_ok": False,
-        "external_ok": False,
-        "internal_status": None,
-        "external_status": None,
-        "diagnosis": "unknown",
-    }
-
-    # Check from inside the container (loopback)
-    internal = subprocess.run(
-        [
-            "docker",
-            "exec",
-            container_name,
-            "sh",
-            "-c",
-            f"curl -s -o /dev/null -w '%{{http_code}}' http://localhost:{port}",
-        ],
-        capture_output=True,
-        text=True,
-        timeout=5,
-    )
-    if internal.returncode == 0:
-        try:
-            result["internal_status"] = int(internal.stdout.strip())
-            result["internal_ok"] = result["internal_status"] > 0
-        except ValueError:
-            pass
-
-    # Check from outside the container (Docker network)
-    external = subprocess.run(
-        [
-            "curl",
-            "-s",
-            "-o",
-            "/dev/null",
-            "-w",
-            "%{http_code}",
-            f"http://{container_name}:{port}",
-        ],
-        capture_output=True,
-        text=True,
-        timeout=5,
-    )
-    if external.returncode == 0:
-        try:
-            result["external_status"] = int(external.stdout.strip())
-            result["external_ok"] = result["external_status"] > 0
-        except ValueError:
-            pass
-
-    # Diagnose binding issue
-    if result["internal_ok"] and not result["external_ok"]:
-        result["diagnosis"] = (
-            f"App appears to be bound to 127.0.0.1:{port} inside the container. "
-            f"It must bind to 0.0.0.0:{port} to be accessible from the tunnel."
-        )
-    elif result["internal_ok"] and result["external_ok"]:
-        result["diagnosis"] = "App is accessible on both interfaces."
-    elif not result["internal_ok"] and not result["external_ok"]:
-        result["diagnosis"] = f"App is not responding on port {port} at all."
-    else:
-        result["diagnosis"] = "Unexpected binding state."
-
-    return result
-
-
-def start_cloudflared_tunnel(
-    container_name: str, port: int, timeout: int = 30
-) -> dict[str, str]:
-    """Start a temporary Cloudflare tunnel for a container.
-
-    Uses 'cloudflared tunnel --url' to create a temporary tunnel
-    with a random trycloudflare.com URL.
-
-    Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        timeout: Maximum seconds to wait for tunnel URL
-
-    Returns:
-        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
-    """
-    import subprocess
-    import logging
-
-    logger = logging.getLogger(__name__)
-
-    # First verify the container is accessible from the Docker network
-    logger.info("Checking connectivity to %s:%d...", container_name, port)
-    accessible = False
-    last_status = None
-    for attempt in range(30):  # 30 attempts × 1s = 30s max wait for app startup
-        check = subprocess.run(
-            [
-                "curl",
-                "-s",
-                "-o",
-                "/dev/null",
-                "-w",
-                "%{http_code}",
-                "--max-time",
-                "3",
-                f"http://{container_name}:{port}",
-            ],
-            capture_output=True,
-            text=True,
-            timeout=5,
-        )
-        status_str = check.stdout.strip()
-        logger.info(
-            "Connectivity check %d/%d: http_code=%s (rc=%d)",
-            attempt + 1,
-            30,
-            status_str,
-            check.returncode,
-        )
-        try:
-            last_status = int(status_str)
-            # Accept 2xx, 3xx, 401, 403 as "app is listening"
-            if last_status in (401, 403) or 200 <= last_status < 400:
-                accessible = True
-                logger.info(
-                    "App on %s:%d is ready (HTTP %d)",
-                    container_name,
-                    port,
-                    last_status,
-                )
-                break
-        except ValueError:
-            pass
-
-        if check.returncode != 0:
-            logger.debug(
-                "curl failed: stderr=%s", check.stderr.strip() if check.stderr else ""
-            )
-        time.sleep(1)
-
-    if not accessible:
-        logger.warning(
-            "Container %s:%d not responding after 30s (last status: %s). "
-            "Running binding diagnostics...",
-            container_name,
-            port,
-            last_status,
-        )
-        diagnosis = _check_app_binding(container_name, port)
-        logger.warning(
-            "Binding diagnosis: internal=%s (HTTP %s), external=%s (HTTP %s). %s",
-            diagnosis["internal_ok"],
-            diagnosis["internal_status"],
-            diagnosis["external_ok"],
-            diagnosis["external_status"],
-            diagnosis["diagnosis"],
-        )
-
-    # Run cloudflared in background, capture output
-    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
-    proc = subprocess.Popen(
-        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        text=True,
-    )
-
-    # Wait for the URL to appear in output
-    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
-    start_time = time.time()
-    url = None
-
-    if proc.stdout is None:
-        proc.terminate()
-        proc.wait(timeout=5)
-        raise RuntimeError("Failed to capture cloudflared output")
-
-    while time.time() - start_time < timeout:
-        # Read available output
-        import select
-
-        readable, _, _ = select.select([proc.stdout], [], [], 1.0)
-        if readable:
-            line = proc.stdout.readline()
-            if line:
-                match = url_pattern.search(line)
-                if match:
-                    url = match.group(0)
-                    break
-
-    if not url:
-        proc.terminate()
-        proc.wait(timeout=5)
-        raise RuntimeError(
-            f"Failed to get tunnel URL within {timeout}s. "
-            f"cloudflared output may contain errors."
-        )
-
-    return {"url": url, "pid": str(proc.pid)}
-
-
-def stop_cloudflared_tunnel(pid: str) -> None:
-    """Stop a cloudflared tunnel process.
-
-    Args:
-        pid: Process ID of the cloudflared tunnel
-    """
-    import signal
-
-    try:
-        os.kill(int(pid), signal.SIGTERM)
-    except ProcessLookupError:
-        pass  # Already stopped
-
-
-def recreate_tunnel(
-    container_name: str, port: int, old_pid: str | None = None
-) -> dict[str, str]:
-    """Recreate a temporary Cloudflare tunnel.
-
-    Stops the old tunnel (if pid provided) and starts a new one.
-
-    Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        old_pid: Optional PID of the old tunnel process to stop
-
-    Returns:
-        Dict with 'url' and 'pid' for the new tunnel
-    """
-    if old_pid:
-        stop_cloudflared_tunnel(old_pid)
-
-    return start_cloudflared_tunnel(container_name, port)
-
-
-def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
-    """Check if a tunnel URL is healthy with smart error classification.
-
-    Args:
-        url: The tunnel URL to check
-        timeout: Request timeout in seconds
-
-    Returns:
-        Dict with 'tunnel_status' (healthy, unreachable, error_response, not_applicable),
-        'status_code' (int or None), 'healthy' (bool), and 'error' (str or None)
-    """
-    import subprocess
-
-    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,
-            }
-        elif status_code in (502, 503, 504):
-            # Application error, not tunnel error
-            return {
-                "tunnel_status": "error_response",
-                "status_code": status_code,
-                "healthy": False,
-                "error": f"Application returned HTTP {status_code}",
-            }
-        else:
-            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 e:
-        error_str = str(e).lower()
-        # Classify connection errors
-        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: {e}",
-            }
-        return {
-            "tunnel_status": "unreachable",
-            "status_code": None,
-            "healthy": False,
-            "error": str(e),
-        }

apps/api/src/services/docker/__init__.py

@@ -0,0 +1,44 @@
+"""Docker services for container and tunnel management."""
+
+from .compose import (
+    ensure_instance_directory,
+    execute_compose_command,
+    render_compose_template,
+    write_compose_file,
+    write_env_file,
+)
+from .config_staging import write_config_files, write_config_folder_files
+from .container import (
+    connect_container_to_network,
+    find_free_port,
+    get_container_id,
+    get_container_logs,
+    get_container_name,
+    get_container_status,
+)
+from .tunnel import (
+    check_tunnel_health,
+    recreate_tunnel,
+    start_cloudflared_tunnel,
+    stop_cloudflared_tunnel,
+)
+
+__all__ = [
+    "render_compose_template",
+    "ensure_instance_directory",
+    "write_compose_file",
+    "write_env_file",
+    "execute_compose_command",
+    "write_config_files",
+    "write_config_folder_files",
+    "get_container_id",
+    "get_container_name",
+    "connect_container_to_network",
+    "get_container_status",
+    "get_container_logs",
+    "find_free_port",
+    "start_cloudflared_tunnel",
+    "stop_cloudflared_tunnel",
+    "recreate_tunnel",
+    "check_tunnel_health",
+]