fix: notification center always on top

The notification dropdown was at z-index: 100, well below fullscreen
terminals (1000), modal overlays (1000), and dialog overlays (1000).
Because .notification-center creates a stacking context with no explicit
z-index, the dropdown was trapped behind any of those overlays and
became unclickable.

- Set .notification-center z-index to 9999 so it competes above all
  other overlays in the root stacking context.
- Set .notification-dropdown z-index to 9999 for consistency.

Quality gates: tsc --noEmit (pass), build (pass)

.atl/.skill-registry.cache.json

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

.atl/skill-registry.md

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

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

@@ -0,0 +1,195 @@
+---
+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

@@ -48,3 +48,9 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
+/.stoneforge/.worktrees/
+# Pi / agent cache
+.pi/
+.atl/
+.sisyphus/
+.pi-lens/

.pi/settings.json

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

.sisyphus/run-continuation/ses_1da2608b1ffergOzow3NQt1mGr.json

@@ -0,0 +1,10 @@
+{
+  "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

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

.stoneforge/.gitignore

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

.stoneforge/config.yaml

@@ -0,0 +1,20 @@
+# 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

@@ -0,0 +1,43 @@
+{"blockedId":"el-1of","blockerId":"el-258","type":"parent-child","createdAt":"2026-05-24T09:44:58.759Z","createdBy":"el-2jua"}
+{"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

@@ -4,6 +4,10 @@
 
 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
@@ -71,6 +75,7 @@ Do not:
 * Introduce new dependencies without clear justification.
 * Treat existing code as more authoritative than OpenSpec for intended behavior.
 * Decide product behavior silently when the spec is unclear.
+* Run `docker compose` commands (build, up, down, etc.) without explicit user approval and proper isolation (e.g., feature branches, separate worktrees, or staged rollouts). Docker Compose operations are deployment-level changes that can affect running services, shared volumes, and network state. Always ask first.
 
 If scope must change, propose an OpenSpec update first.
 
@@ -87,6 +92,31 @@ 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:

apps/api/.dockerignore

@@ -0,0 +1,42 @@
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Test artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Git
+.git/
+.gitignore
+
+# Local env files
+.env
+.env.local
+
+# Alembic cache
+alembic/versions/__pycache__/
+
+# Pi lens cache
+.pi-lens/
+
+# Documentation
+docs/
+*.md
+
+# Scripts not needed in container
+scripts/

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

@@ -0,0 +1,568 @@
+{
+  "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

@@ -16,34 +16,51 @@ RUN pip install --no-cache-dir --user -e ".[dev]"
 # Production stage
 FROM python:3.11-slim
 
-# Create non-root user
-RUN groupadd -r appgroup && useradd -r -g appgroup appuser
+# Create non-root user and add to docker group
+RUN groupadd -r appgroup && useradd -r -g appgroup appuser \
+    && groupadd -r docker || true \
+    && usermod -aG docker appuser
 
 WORKDIR /app
 
-# Install runtime dependencies
+# Install runtime dependencies including Docker CLI
 RUN apt-get update && apt-get install -y --no-install-recommends \
     libpq5 \
     git \
+    openssh-client \
     netcat-openbsd \
+    ca-certificates \
+    curl \
+    gnupg \
+    && install -m 0755 -d /etc/apt/keyrings \
+    && curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg \
+    && chmod a+r /etc/apt/keyrings/docker.gpg \
+    && echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
+    "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" > /etc/apt/sources.list.d/docker.list \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends docker-ce-cli docker-compose-plugin \
+    && curl -L --output /usr/local/bin/cloudflared https://github.com/cloudflare/cloudflared/releases/latest/download/cloudflared-linux-amd64 \
+    && chmod +x /usr/local/bin/cloudflared \
     && rm -rf /var/lib/apt/lists/*
 
 # Copy dependencies from builder
-COPY --from=builder /root/.local /home/appuser/.local
-ENV PATH=/home/appuser/.local/bin:$PATH
+COPY --from=builder /root/.local /root/.local
+ENV PATH=/root/.local/bin:$PATH
 
 # Copy application code
 COPY --chown=appuser:appgroup . .
 
-# Create directories for repo storage
-RUN mkdir -p /data/repos && chown -R appuser:appgroup /data/repos
+# Create directories for repo, instance, and workspace storage
+RUN mkdir -p /data/repos /data/instances /data/working-copies && chown -R appuser:appgroup /data
 
 # Copy wait-for-db script
 COPY wait-for-db.sh /usr/local/bin/wait-for-db.sh
 RUN chmod +x /usr/local/bin/wait-for-db.sh
 
-# Switch to non-root user
-USER appuser
+# NOTE: Running as root to access Docker socket for managing tool instances
+# This is required because Docker socket permissions require root or docker group membership
+# which doesn't work well across container boundaries.
+# Consider using Docker-in-Docker or rootless Docker for production hardening.
 
 # Expose port
 EXPOSE 8000

apps/api/README.md

@@ -0,0 +1,252 @@
+# Headquarter API
+
+The backend API for Headquarter - a self-hosted platform for managing projects, git repositories, and development tools.
+
+## Overview
+
+Built with **FastAPI** and **SQLAlchemy** (async), using **PostgreSQL** for data storage and **Docker** for tool instance management.
+
+### Tech Stack
+
+- **Framework**: FastAPI (Python 3.12+)
+- **Database**: PostgreSQL 15+ with asyncpg
+- **ORM**: SQLAlchemy 2.0 (async)
+- **Auth**: OAuth2 via Authentik with session cookies
+- **Migrations**: Alembic
+- **Tools**: Docker Compose for instance management
+
+## Quick Start
+
+### Prerequisites
+
+- Python 3.12+
+- PostgreSQL 15+ running locally
+- Docker (for tool instances)
+
+### Setup
+
+```bash
+cd apps/api
+
+# Create virtual environment
+python -m venv .venv
+source .venv/bin/activate
+
+# Install dependencies
+pip install -e ".[dev]"
+
+# Set up database
+# Ensure PostgreSQL is running with a 'headquarter' database
+
+# Run migrations
+alembic upgrade head
+
+# Start development server
+uvicorn src.main:app --reload --port 8000
+```
+
+The API will be available at `http://localhost:8000`.
+
+### Interactive Documentation
+
+Once running, visit:
+- **Swagger UI**: http://localhost:8000/docs
+- **ReDoc**: http://localhost:8000/redoc
+- **OpenAPI JSON**: http://localhost:8000/openapi.json
+
+## Environment Variables
+
+| Variable | Required | Default | Description |
+|----------|----------|---------|-------------|
+| `DATABASE_URL` | Yes | - | PostgreSQL connection string |
+| `API_BASE_URL` | Yes | - | Public API URL (e.g., `https://api.example.com`) |
+| `AUTHENTIK_DOMAIN` | Yes | - | Authentik server domain |
+| `AUTHENTIK_CLIENT_ID` | Yes | - | OAuth2 client ID |
+| `AUTHENTIK_CLIENT_SECRET` | Yes | - | OAuth2 client secret |
+| `AUTHENTIK_APPLICATION_SLUG` | Yes | - | Authentik application slug |
+| `WEB_BASE_URL` | Yes | - | Public frontend URL |
+| `SESSION_SECRET` | Yes | - | Secret for session cookie signing |
+| `COOKIE_DOMAIN` | No | - | Cookie domain (e.g., `.example.com`) |
+| `UPLOAD_DIR` | No | `./uploads` | Directory for file uploads |
+| `REPO_BASE_PATH` | No | `./repositories` | Base path for git repositories |
+| `INSTANCES_BASE_PATH` | No | `./instances` | Base path for tool instances |
+| `LOG_LEVEL` | No | `INFO` | Logging level |
+
+## Development
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run specific test category
+pytest -m unit          # Unit tests (no DB)
+pytest -m integration   # Integration tests (requires DB)
+
+# Run with coverage
+pytest --cov=src --cov-report=html
+```
+
+### Code Quality
+
+```bash
+# Format code
+ruff format src tests
+
+# Lint
+ruff check src tests
+
+# Type check
+mypy src
+```
+
+### Database Migrations
+
+```bash
+# Create new migration
+alembic revision --autogenerate -m "description"
+
+# Apply migrations
+alembic upgrade head
+
+# Rollback one migration
+alembic downgrade -1
+
+# Show current revision
+alembic current
+```
+
+## Architecture
+
+### Directory Structure
+
+```
+src/
+├── api/              # API endpoint routers
+│   ├── auth.py       # OAuth2 authentication
+│   ├── dashboard.py  # Dashboard summary
+│   ├── git_repositories.py  # Git repo management
+│   ├── health.py     # Health checks
+│   ├── projects.py   # Project CRUD
+│   ├── ssh_keys.py   # SSH key management
+│   ├── terminal.py   # WebSocket terminal
+│   ├── tool_instances.py  # Tool instance management
+│   ├── tool_types.py # Tool type definitions
+│   ├── user_config.py # User preferences
+│   └── users.py      # User profile
+├── auth/             # Authentication logic
+│   ├── cookies.py    # Cookie utilities
+│   ├── dependencies.py # Auth dependencies
+│   ├── oidc.py       # OpenID Connect
+│   └── session.py    # Session management
+├── config.py         # Application settings
+├── database.py       # Database setup
+├── main.py           # FastAPI application
+├── models/           # SQLAlchemy models
+├── schemas/          # Pydantic schemas
+├── services/         # Business logic
+│   ├── docker.py     # Docker Compose management
+│   ├── terminal_manager.py  # Terminal sessions
+│   └── terminal_session.py  # Terminal I/O
+└── utils/            # Utilities
+    ├── git_control.py      # Git operations
+    ├── git_files.py        # File operations
+    ├── git_history.py      # History extraction
+    └── git_url_parser.py   # URL parsing
+```
+
+### Authentication Flow
+
+1. User clicks "Login" → redirects to Authentik OAuth
+2. Authentik redirects back with authorization code
+3. API exchanges code for tokens and fetches user info
+4. API creates session cookie (HMAC-signed, httpOnly)
+5. Frontend stores nothing - cookie sent automatically
+6. Subsequent requests include cookie for authentication
+
+### Data Flow
+
+```
+Client → FastAPI Router → Auth Dependency → Service Layer → Database
+                ↓
+         Pydantic Models (validation)
+                ↓
+         SQLAlchemy Models (ORM)
+                ↓
+         PostgreSQL (storage)
+```
+
+## API Endpoints
+
+### Authentication
+- `GET /auth/login` - Initiate OAuth login
+- `GET /auth/callback` - OAuth callback
+- `GET /auth/me` - Get current user
+- `POST /auth/logout` - Logout
+
+### Projects
+- `GET /projects` - List projects
+- `POST /projects` - Create project
+- `GET /projects/{id}` - Get project
+- `PUT /projects/{id}` - Update project
+- `DELETE /projects/{id}` - Delete project
+
+### Git Repositories
+- `GET /projects/{id}/repositories` - List repositories
+- `POST /projects/{id}/repositories` - Create repository
+- `GET /projects/{id}/repositories/{id}` - Get repository
+- `DELETE /projects/{id}/repositories/{id}` - Delete repository
+- `GET /projects/{id}/repositories/{id}/files` - List files
+- `GET /projects/{id}/repositories/{id}/files/content` - Get file content
+- `POST /projects/{id}/repositories/{id}/files/content` - Update file
+- `GET /projects/{id}/repositories/{id}/branches` - List branches
+- `GET /projects/{id}/repositories/{id}/history` - Commit history
+- `GET /projects/{id}/repositories/{id}/commits/{hash}` - Commit detail
+
+### Tool Types
+- `GET /tool-types` - List tool types
+- `POST /tool-types` - Create tool type
+- `GET /tool-types/{id}` - Get tool type
+- `PUT /tool-types/{id}` - Update tool type
+- `DELETE /tool-types/{id}` - Delete tool type
+
+### Tool Instances
+- `GET /tool-instances` - List instances
+- `POST /tool-instances` - Create instance
+- `GET /tool-instances/{id}` - Get instance
+- `POST /tool-instances/{id}/start` - Start instance
+- `POST /tool-instances/{id}/stop` - Stop instance
+- `POST /tool-instances/{id}/restart` - Restart instance
+- `DELETE /tool-instances/{id}` - Delete instance
+- `GET /tool-instances/{id}/logs` - Get logs
+
+### Terminal
+- `WS /ws/tool-instances/{id}/terminal` - WebSocket terminal
+
+### Users
+- `GET /users/me` - Get profile
+- `PUT /users/me` - Update profile
+- `POST /users/me/avatar` - Upload avatar
+- `GET /users/me/config` - Get config
+- `PATCH /users/me/config` - Update config
+
+### SSH Keys
+- `GET /ssh-keys` - List keys
+- `POST /ssh-keys` - Create key
+- `DELETE /ssh-keys/{id}` - Delete key
+
+### Health
+- `GET /health` - System health
+- `GET /health/db` - Database health
+
+## Deployment
+
+See the [deployment documentation](../../docs/deployment/) for Docker and Traefik setup.
+
+## Contributing
+
+1. Follow PEP 8 style guide
+2. Add tests for new endpoints
+3. Update documentation
+4. Run quality gates before committing

apps/api/alembic/versions/0007_instance_container_name.py

@@ -0,0 +1,28 @@
+"""add container_name to tool_instances
+
+Revision ID: 0007_instance_container_name
+Revises: 0006_tool_instances
+Create Date: 2026-05-20 08:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0007_instance_container_name"
+down_revision: Union[str, None] = "0006_tool_instances"
+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("container_name", sa.String(255), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "container_name")

apps/api/alembic/versions/0008_tool_type_category.py

@@ -0,0 +1,33 @@
+"""add category and interfaces to tool_types
+
+Revision ID: 0008_tool_type_category
+Revises: 0007_instance_container_name
+Create Date: 2026-05-20 09:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0008_tool_type_category"
+down_revision: Union[str, None] = "0007_instance_container_name"
+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("category", sa.String(50), nullable=False, server_default="other")
+    )
+    op.add_column(
+        "tool_types",
+        sa.Column("interfaces", sa.JSON(), nullable=False, server_default='["web"]')
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_types", "interfaces")
+    op.drop_column("tool_types", "category")

apps/api/alembic/versions/0009_tool_configs.py

@@ -0,0 +1,46 @@
+"""add tool_configs table
+
+Revision ID: 0009_tool_configs
+Revises: 0008_tool_type_category
+Create Date: 2026-05-20 09:00:00.000000
+
+"""
+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 = "0009_tool_configs"
+down_revision: Union[str, None] = "0008_tool_type_category"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "tool_configs",
+        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), nullable=False),
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+        sa.Column("key", sa.String(255), nullable=False),
+        sa.Column("value", sa.Text(), nullable=False),
+        sa.Column("config_type", sa.String(20), nullable=False, server_default="env"),
+        sa.Column("file_path", sa.String(1024), 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"]),
+        sa.ForeignKeyConstraint(["tool_type_id"], ["tool_types.id"]),
+        sa.ForeignKeyConstraint(["project_id"], ["projects.id"]),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_tool_configs_user_tool", "tool_configs", ["user_id", "tool_type_id"])
+    op.create_index("idx_tool_configs_project", "tool_configs", ["project_id"])
+
+
+def downgrade() -> None:
+    op.drop_index("idx_tool_configs_project", table_name="tool_configs")
+    op.drop_index("idx_tool_configs_user_tool", table_name="tool_configs")
+    op.drop_table("tool_configs")

apps/api/alembic/versions/0010_tool_type_default_port.py

@@ -0,0 +1,28 @@
+"""add default_port to tool_types
+
+Revision ID: 0010_tool_type_default_port
+Revises: 0009_tool_configs
+Create Date: 2026-05-20 10:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0010_tool_type_default_port"
+down_revision: Union[str, None] = "0009_tool_configs"
+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("default_port", sa.Integer(), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_types", "default_port")

apps/api/alembic/versions/0011_tool_instance_tunnel_fields.py

@@ -0,0 +1,33 @@
+"""add tunnel fields to tool_instances
+
+Revision ID: 0011_tool_instance_tunnel_fields
+Revises: 0010_tool_type_default_port
+Create Date: 2026-05-20 12:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0011_tool_instance_tunnel_fields"
+down_revision: Union[str, None] = "0010_tool_type_default_port"
+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("public_url", sa.String(1024), nullable=True)
+    )
+    op.add_column(
+        "tool_instances",
+        sa.Column("tunnel_id", sa.String(255), nullable=True)
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "tunnel_id")
+    op.drop_column("tool_instances", "public_url")

apps/api/alembic/versions/0012_default_port_req.py

@@ -0,0 +1,48 @@
+"""make default_port non-nullable and set values
+
+Revision ID: 0012_default_port_req
+Revises: 0011_tool_instance_tunnel_fields
+Create Date: 2026-05-20 15:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "0012_default_port_req"
+down_revision: Union[str, None] = "0011_tool_instance_tunnel_fields"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Set default_port for existing built-in tool types
+    op.execute("""
+        UPDATE tool_types 
+        SET default_port = CASE 
+            WHEN name = 'code-server' THEN 8443
+            WHEN name = 'jupyter-notebook' THEN 8888
+            WHEN name = 'opencode' THEN 3000
+            ELSE 8080
+        END
+        WHERE default_port IS NULL
+    """)
+    
+    # Make default_port non-nullable
+    op.alter_column(
+        "tool_types",
+        "default_port",
+        existing_type=sa.Integer(),
+        nullable=False,
+    )
+
+
+def downgrade() -> None:
+    op.alter_column(
+        "tool_types",
+        "default_port",
+        existing_type=sa.Integer(),
+        nullable=True,
+    )

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

@@ -0,0 +1,204 @@
+"""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 collections.abc import Sequence
+
+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: str | None = "0012_default_port_req"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def upgrade() -> None:
+    # Earlier branches may already have created config_profiles. Keep this
+    # migration defensive so databases can converge onto the current graph.
+    if not _table_exists("config_profiles"):
+        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"
+            ),
+        )
+    if not _index_exists("config_profiles", "idx_config_profiles_user"):
+        op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+
+    if not _table_exists("config_includes"):
+        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"
+            ),
+        )
+    if not _index_exists("config_includes", "idx_config_includes_profile"):
+        op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    if not _index_exists("config_includes", "idx_config_includes_included"):
+        op.create_index(
+            "idx_config_includes_included", "config_includes", ["included_profile_id"]
+        )
+
+    if not _table_exists("config_mounts"):
+        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"),
+        )
+    if not _index_exists("config_mounts", "idx_config_mounts_profile"):
+        op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+
+    if not _column_exists("tool_instances", "selected_profile_id"):
+        op.add_column(
+            "tool_instances",
+            sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _foreign_key_exists(
+        "tool_instances", ["selected_profile_id"], "config_profiles"
+    ):
+        op.create_foreign_key(
+            "fk_tool_instances_selected_profile",
+            "tool_instances",
+            "config_profiles",
+            ["selected_profile_id"],
+            ["id"],
+            ondelete="SET NULL",
+        )
+    if not _index_exists("tool_instances", "idx_tool_instances_selected_profile"):
+        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

@@ -0,0 +1,29 @@
+"""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 +1,180 @@
+"""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 collections.abc import Sequence
+
+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: str | None = "0013_add_config_profiles"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def _foreign_key_names_for_column(table_name: str, column_name: str) -> list[str]:
+    if not _table_exists(table_name):
+        return []
+    names: list[str] = []
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if column_name in foreign_key.get("constrained_columns", []):
+            name = foreign_key.get("name")
+            if name:
+                names.append(name)
+    return names
+
+
+def upgrade() -> None:
+    if not _column_exists("config_profiles", "project_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "tool_type_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "environment_variables"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("environment_variables", sa.JSON(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "start_command"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("start_command", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "working_directory"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("working_directory", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "port"):
+        op.add_column("config_profiles", sa.Column("port", sa.Integer(), nullable=True))
+    if not _column_exists("config_profiles", "is_default"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+        )
+
+    if not _foreign_key_exists("config_profiles", ["project_id"], "projects"):
+        op.create_foreign_key(
+            "fk_config_profiles_project",
+            "config_profiles",
+            "projects",
+            ["project_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+    if not _foreign_key_exists("config_profiles", ["tool_type_id"], "tool_types"):
+        op.create_foreign_key(
+            "fk_config_profiles_tool_type",
+            "config_profiles",
+            "tool_types",
+            ["tool_type_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+
+    if not _index_exists("config_profiles", "idx_config_profiles_project"):
+        op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    if not _index_exists("config_profiles", "idx_config_profiles_tool_type"):
+        op.create_index(
+            "idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"]
+        )
+
+    if _column_exists("config_mounts", "mount_path") and not _column_exists(
+        "config_mounts", "target_path"
+    ):
+        op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
+    if not _column_exists("config_mounts", "mode"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
+        )
+    if not _column_exists("config_mounts", "files"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("files", sa.JSON(), nullable=True),
+        )
+    for constraint_name in _foreign_key_names_for_column(
+        "config_mounts", "source_profile_id"
+    ):
+        op.drop_constraint(constraint_name, "config_mounts", type_="foreignkey")
+    if _column_exists("config_mounts", "content"):
+        op.drop_column("config_mounts", "content")
+    if _column_exists("config_mounts", "source_profile_id"):
+        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

@@ -0,0 +1,23 @@
+"""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

@@ -0,0 +1,109 @@
+"""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

@@ -0,0 +1,32 @@
+"""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

@@ -0,0 +1,129 @@
+"""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

@@ -0,0 +1,36 @@
+"""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

@@ -0,0 +1,25 @@
+"""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

@@ -0,0 +1,30 @@
+"""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

@@ -0,0 +1,86 @@
+"""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

@@ -0,0 +1,28 @@
+"""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

@@ -0,0 +1,41 @@
+"""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

@@ -0,0 +1,122 @@
+"""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

@@ -0,0 +1,61 @@
+"""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

@@ -0,0 +1,373 @@
+"""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

@@ -0,0 +1,89 @@
+"""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

@@ -0,0 +1,69 @@
+"""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

@@ -0,0 +1,27 @@
+"""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

@@ -0,0 +1,32 @@
+"""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

@@ -0,0 +1,54 @@
+"""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

@@ -0,0 +1,148 @@
+"""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

@@ -0,0 +1,140 @@
+"""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

@@ -0,0 +1,121 @@
+"""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

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

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

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

apps/api/alembic/versions/398082499c30_add_tool_config_fields.py

@@ -0,0 +1,40 @@
+"""add_tool_config_fields
+
+Revision ID: 398082499c30
+Revises: af8512103d67
+Create Date: 2026-05-22 18:38:20.166184
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '398082499c30'
+down_revision = 'af8512103d67'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Add new columns to tool_configs
+    op.add_column('tool_configs', sa.Column('port_override', sa.Integer(), nullable=True))
+    op.add_column('tool_configs', sa.Column('start_command', sa.Text(), nullable=True))
+    op.add_column('tool_configs', sa.Column('working_directory', sa.Text(), nullable=True))
+    op.add_column('tool_configs', sa.Column('environment_variables', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'))
+    op.add_column('tool_configs', sa.Column('volumes', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='[]'))
+    
+    # Add CHECK constraint for port range
+    op.create_check_constraint('chk_port_range', 'tool_configs', sa.text('port_override IS NULL OR (port_override >= 1 AND port_override <= 65535)'))
+
+
+def downgrade() -> None:
+    # Drop CHECK constraint
+    op.drop_constraint('chk_port_range', 'tool_configs', type_='check')
+    
+    # Drop columns
+    op.drop_column('tool_configs', 'port_override')
+    op.drop_column('tool_configs', 'start_command')
+    op.drop_column('tool_configs', 'working_directory')
+    op.drop_column('tool_configs', 'environment_variables')
+    op.drop_column('tool_configs', 'volumes')

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

@@ -0,0 +1,23 @@
+"""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/86cec91fdb00_merge_profile_resolver_and_workspaces_.py

@@ -0,0 +1,20 @@
+"""merge profile resolver and workspaces heads
+
+Revision ID: 86cec91fdb00
+Revises: 0014_add_profile_resolver_fields, 2026_06_01_add_workspaces
+Create Date: 2026-06-03 12:48:36.145702
+"""
+
+# revision identifiers, used by Alembic.
+revision = "86cec91fdb00"
+down_revision = ("0014_add_profile_resolver_fields", "2026_06_01_add_workspaces")
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/8ed7dd80973d_create_config_folders_table.py

@@ -0,0 +1,44 @@
+"""create_config_folders_table
+
+Revision ID: 8ed7dd80973d
+Revises: 398082499c30
+Create Date: 2026-05-22 18:38:22.133696
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '8ed7dd80973d'
+down_revision = '398082499c30'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        'config_folders',
+        sa.Column('id', postgresql.UUID(as_uuid=True), primary_key=True, server_default=sa.text('gen_random_uuid()')),
+        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('mount_path', sa.String(1024), nullable=False),
+        sa.Column('files', postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='{}'),
+        sa.Column('project_overrides', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'),
+        sa.Column('is_active', sa.Boolean(), nullable=False, server_default='true'),
+        sa.Column('created_at', sa.DateTime(timezone=True), nullable=False, server_default=sa.text('NOW()')),
+        sa.Column('updated_at', sa.DateTime(timezone=True), nullable=False, server_default=sa.text('NOW()')),
+        sa.UniqueConstraint('user_id', 'name', name='uq_config_folders_user_name')
+    )
+    
+    # Add index on user_id for filtering
+    op.create_index('idx_config_folders_user', 'config_folders', ['user_id'])
+
+
+def downgrade() -> None:
+    # Drop index
+    op.drop_index('idx_config_folders_user', table_name='config_folders')
+    
+    # Drop table
+    op.drop_table('config_folders')

apps/api/alembic/versions/af8512103d67_add_tool_type_fields.py

@@ -0,0 +1,38 @@
+"""add_tool_type_fields
+
+Revision ID: af8512103d67
+Revises: 0012_default_port_req
+Create Date: 2026-05-22 18:37:56.607240
+"""
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = 'af8512103d67'
+down_revision = '0012_default_port_req'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # Add new columns to tool_types
+    op.add_column('tool_types', sa.Column('definition_type', sa.String(20), nullable=False, server_default='compose'))
+    op.add_column('tool_types', sa.Column('dockerfile_template', sa.Text(), nullable=True))
+    op.add_column('tool_types', sa.Column('build_context', postgresql.JSONB(astext_type=sa.Text()), nullable=True, server_default='{}'))
+    op.add_column('tool_types', sa.Column('readiness_probe', postgresql.JSONB(astext_type=sa.Text()), nullable=True))
+    
+    # Add CHECK constraint for definition_type
+    op.create_check_constraint('chk_definition_type', 'tool_types', sa.text("definition_type IN ('compose', 'dockerfile')"))
+
+
+def downgrade() -> None:
+    # Drop CHECK constraint
+    op.drop_constraint('chk_definition_type', 'tool_types', type_='check')
+    
+    # Drop columns
+    op.drop_column('tool_types', 'definition_type')
+    op.drop_column('tool_types', 'dockerfile_template')
+    op.drop_column('tool_types', 'build_context')
+    op.drop_column('tool_types', 'readiness_probe')

apps/api/alembic/versions/f3d2dc90ba3a_merge_single_interface_and_clone_mode.py

@@ -0,0 +1,23 @@
+"""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

@@ -1,4 +1 @@
-from src.api.auth import router as auth_router
-from src.api.users import router as users_router
-
-__all__ = ["auth_router", "users_router"]
+"""API routers package."""

apps/api/src/api/config/__init__.py

@@ -0,0 +1,6 @@
+"""Config API routers module."""
+
+from src.api.config.config_profiles import router as config_profiles_router
+from src.api.config.user_config import router as user_config_router
+
+__all__ = ["config_profiles_router", "user_config_router"]

apps/api/src/api/config/config_profiles.py

@@ -0,0 +1,842 @@
+"""Config profile API endpoints."""
+
+import logging
+import os
+import subprocess
+import uuid
+from typing import Any
+
+from fastapi import APIRouter, Depends, HTTPException, Query, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models import ConfigProfile, ConfigProfileInclude
+from src.models.project import Project
+from src.models import ToolType
+from src.models import UserConfig
+from src.schemas.config import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+from src.services.config.config_profile_resolver import (
+    ConfigProfileCycleError,
+    check_include_cycle,
+    resolve_profile,
+    resolved_profile_to_dict,
+)
+from src.utils.git_url_parser import parse_git_url
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
+
+MAX_PROFILE_SIZE_MB = 10
+MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
+
+
+def _calculate_profile_size(data: dict) -> int:
+    """Calculate approximate serialized size of profile data."""
+    total = 0
+    for key, value in data.get("env_vars", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for key, value in data.get("runtime_hints", {}).items():
+        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
+    for mount in data.get("mounts", []):
+        total += len(str(mount.get("target", "")).encode("utf-8"))
+        total += len(str(mount.get("mode", "")).encode("utf-8"))
+        for path, content in mount.get("files", {}).items():
+            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    for path, content in data.get("files", {}).items():
+        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
+    return total
+
+
+async def _get_profile_with_includes(
+    session: AsyncSession, profile_id: uuid.UUID
+) -> ConfigProfile | None:
+    """Fetch a profile with includes eagerly loaded."""
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile_id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    return result.scalar_one_or_none()
+
+
+async def _check_access(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    project_id: uuid.UUID | None = None,
+    tool_type_id: uuid.UUID | None = None,
+) -> None:
+    """Verify user has access to referenced project and tool type."""
+    if project_id is not None:
+        project = await session.get(Project, project_id)
+        if project is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="Project not found"
+            )
+        # Add ownership check if needed; for now just verify existence
+    if tool_type_id is not None:
+        tool_type = await session.get(ToolType, tool_type_id)
+        if tool_type is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="Tool type not found"
+            )
+
+
+async def _validate_git_mounts(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+    git_mounts: list[Any],
+    project_id: uuid.UUID | None = None,
+) -> None:
+    """Validate git mount URLs.
+
+    Simply checks that remote_url looks like a valid git URL.
+    Actual clone validation happens at instance startup time.
+    """
+    for mount in git_mounts:
+        remote_url = mount.get("remote_url")
+        if not remote_url:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Git mount missing remote_url",
+            )
+
+        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid git URL: {remote_url}",
+            )
+
+
+def _profile_to_response(
+    profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None
+) -> dict:
+    return {
+        "id": str(profile.id),
+        "user_id": str(profile.user_id),
+        "name": profile.name,
+        "description": profile.description,
+        "project_id": str(profile.project_id) if profile.project_id else None,
+        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
+        "env_vars": profile.env_vars or {},
+        "runtime_hints": profile.runtime_hints or {},
+        "mounts": profile.mounts or [],
+        "git_mounts": profile.git_mounts or [],
+        "files": profile.files or {},
+        "is_default": profile.is_default,
+        "includes": [
+            {
+                "id": str(inc.id),
+                "included_profile_id": str(inc.included_profile_id),
+                "order_index": inc.order_index,
+            }
+            for inc in (includes or profile.includes)
+        ],
+        "created_at": profile.created_at.isoformat() if profile.created_at else None,
+        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
+    }
+
+
+@router.get("", response_model=list[ConfigProfileResponse])
+async def list_config_profiles(
+    project_id: str | None = Query(None, description="Filter by project compatibility"),
+    tool_type_id: str | None = Query(
+        None, description="Filter by tool type compatibility"
+    ),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """List config profiles, optionally filtered by compatibility."""
+    user_uuid = current_user_id
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .options(selectinload(ConfigProfile.includes))
+    )
+
+    if project_id or tool_type_id:
+        # Compatibility filter: include portable profiles and matching scoped profiles
+        project_uuid = uuid.UUID(project_id) if project_id else None
+        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
+
+        from sqlalchemy import or_
+
+        conditions: list = []
+        # Portable profiles (no project, no tool)
+        conditions.append(
+            (ConfigProfile.project_id.is_(None))
+            & (ConfigProfile.tool_type_id.is_(None))
+        )
+        if project_uuid:
+            # Profiles matching this project (with or without tool)
+            conditions.append(ConfigProfile.project_id == project_uuid)
+        if tool_uuid:
+            # Profiles matching this tool (with or without project)
+            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
+        if project_uuid and tool_uuid:
+            # Exact match
+            conditions.append(
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+
+        query = query.where(or_(*conditions))
+
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+    return [_profile_to_response(p) for p in profiles]
+
+
+@router.post(
+    "", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED
+)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Create a new config profile."""
+    user_uuid = current_user_id
+
+    # Check for duplicate name
+    existing = await session.execute(
+        select(ConfigProfile)
+        .where(
+            ConfigProfile.user_id == user_uuid,
+            ConfigProfile.name == data.name,
+        )
+        .options(selectinload(ConfigProfile.includes))
+    )
+    if existing.scalar_one_or_none() is not None:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"Profile with name '{data.name}' already exists",
+        )
+
+    # Validate references
+    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
+    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
+    await _check_access(session, user_uuid, project_uuid, tool_uuid)
+
+    # Validate git mounts reference existing repositories
+    if data.git_mounts:
+        git_mounts_data = [
+            m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts
+        ]
+        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
+
+    # Check size
+    size = _calculate_profile_size(data.model_dump())
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    profile = ConfigProfile(
+        user_id=user_uuid,
+        name=data.name,
+        description=data.description,
+        project_id=project_uuid,
+        tool_type_id=tool_uuid,
+        env_vars=data.env_vars,
+        runtime_hints=data.runtime_hints,
+        mounts=[m.model_dump() for m in data.mounts],
+        git_mounts=[m.model_dump() for m in data.git_mounts],
+        files=data.files,
+        is_default=data.is_default,
+    )
+    session.add(profile)
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
+    return _profile_to_response(profile)
+
+
+@router.get("/{profile_id}", response_model=ConfigProfileResponse)
+async def get_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Get a config profile by ID."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+    return _profile_to_response(profile)
+
+
+@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+async def update_config_profile(
+    profile_id: str,
+    data: ConfigProfileUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    update_data = data.model_dump(exclude_unset=True)
+
+    # Handle name uniqueness
+    if "name" in update_data:
+        existing = await session.execute(
+            select(ConfigProfile).where(
+                ConfigProfile.user_id == profile.user_id,
+                ConfigProfile.name == update_data["name"],
+                ConfigProfile.id != profile.id,
+            )
+        )
+        if existing.scalar_one_or_none() is not None:
+            raise HTTPException(
+                status_code=status.HTTP_409_CONFLICT,
+                detail=f"Profile with name '{update_data['name']}' already exists",
+            )
+
+    # Validate references
+    project_uuid = (
+        uuid.UUID(update_data["project_id"])
+        if "project_id" in update_data and update_data["project_id"]
+        else (profile.project_id if "project_id" not in update_data else None)
+    )
+    tool_uuid = (
+        uuid.UUID(update_data["tool_type_id"])
+        if "tool_type_id" in update_data and update_data["tool_type_id"]
+        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
+    )
+    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
+
+    # Validate git mounts reference existing repositories
+    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
+        git_mounts_data = [
+            m.model_dump() if hasattr(m, "model_dump") else m
+            for m in update_data["git_mounts"]
+        ]
+        await _validate_git_mounts(
+            session, profile.user_id, git_mounts_data, project_uuid
+        )
+
+    # Check size
+    current_data = _profile_to_response(profile)
+    merged = {**current_data, **update_data}
+    size = _calculate_profile_size(merged)
+    if size > MAX_PROFILE_SIZE_BYTES:
+        raise HTTPException(
+            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
+        )
+
+    # Apply updates
+    for field_name, value in update_data.items():
+        if field_name in ("project_id", "tool_type_id"):
+            value = uuid.UUID(value) if value else None
+        elif field_name == "mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        elif field_name == "git_mounts" and value is not None:
+            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
+        setattr(profile, field_name, value)
+
+    await session.commit()
+
+    # Re-fetch with includes to avoid lazy loading issues
+    result = await session.execute(
+        select(ConfigProfile)
+        .where(ConfigProfile.id == profile.id)
+        .options(selectinload(ConfigProfile.includes))
+    )
+    profile = result.scalar_one()
+
+    logger.debug("Updated config profile %s", profile.id)
+    return _profile_to_response(profile)
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Delete a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    await session.delete(profile)
+    await session.commit()
+
+    logger.debug("Deleted config profile %s", profile_id)
+    return None
+
+
+@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
+async def update_profile_includes(
+    profile_id: str,
+    data: ConfigProfileIncludeUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update the ordered includes for a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    # Validate all included profiles exist and belong to the user
+    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
+    for inc_uuid in included_uuids:
+        inc_profile = await session.get(ConfigProfile, inc_uuid)
+        if inc_profile is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Included profile not found: {inc_uuid}",
+            )
+        if inc_profile.user_id != current_user_id:
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail=f"Not authorized to include profile: {inc_uuid}",
+            )
+        if inc_uuid == profile.id:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="Profile cannot include itself",
+            )
+
+    # Check for cycles
+    cycle = await check_include_cycle(session, profile.id, None)
+    if cycle is None and included_uuids:
+        # Check each new include would not create a cycle
+        for inc_uuid in included_uuids:
+            cycle = await check_include_cycle(session, profile.id, inc_uuid)
+            if cycle is not None:
+                break
+
+    if cycle is not None:
+        cycle_str = " -> ".join(str(c) for c in cycle)
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Include cycle detected: {cycle_str}",
+        )
+
+    # Remove existing includes
+    result = await session.execute(
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
+    )
+    for existing in result.scalars().all():
+        await session.delete(existing)
+    await session.flush()
+
+    # Add new includes
+    for order_index, inc_uuid in enumerate(included_uuids):
+        include = ConfigProfileInclude(
+            profile_id=profile.id,
+            included_profile_id=inc_uuid,
+            order_index=order_index,
+        )
+        session.add(include)
+    await session.flush()
+
+    await session.commit()
+
+    # Re-fetch profile (includes loaded separately due to SQLite async issue)
+    result = await session.execute(
+        select(ConfigProfile).where(ConfigProfile.id == profile.id)
+    )
+    profile = result.scalar_one()
+
+    inc_result = await session.execute(
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
+    )
+    direct_includes = inc_result.scalars().all()
+
+    logger.debug("Updated includes for config profile %s", profile.id)
+    return _profile_to_response(profile, list(direct_includes))
+
+
+@router.get("/{profile_id}/preview")
+async def preview_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Preview the resolved output of a config profile."""
+    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    try:
+        resolved = await resolve_profile(session, profile.id)
+    except ConfigProfileCycleError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=str(exc),
+        )
+
+    return resolved_profile_to_dict(resolved)
+
+
+@router.get("/defaults/resolve")
+async def resolve_default_profile(
+    project_id: str = Query(..., description="Project ID"),
+    tool_type_id: str = Query(..., description="Tool type ID"),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Resolve the default config profile for a project/tool combination.
+
+    Selects by specificity:
+    1. project+tool explicit default
+    2. project explicit default
+    3. tool explicit default
+    4. global/user explicit default
+    5. first created compatible profile
+    6. none (returns null)
+    """
+    user_uuid = current_user_id
+    project_uuid = uuid.UUID(project_id)
+    tool_uuid = uuid.UUID(tool_type_id)
+
+    # Fetch all compatible profiles ordered by created_at
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .where(
+            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
+            | (ConfigProfile.project_id == project_uuid)
+            | (ConfigProfile.tool_type_id == tool_uuid)
+            | (
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+        )
+        .order_by(ConfigProfile.created_at)
+    )
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+
+    if not profiles:
+        return {"profile_id": None, "profile_name": None}
+
+    # Check explicit defaults by specificity
+    explicit_defaults = [p for p in profiles if p.is_default]
+
+    # Most specific: project+tool
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: project only
+    for p in explicit_defaults:
+        if p.project_id == project_uuid and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: tool only
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id == tool_uuid:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Next: global/user (no project, no tool)
+    for p in explicit_defaults:
+        if p.project_id is None and p.tool_type_id is None:
+            return {"profile_id": str(p.id), "profile_name": p.name}
+
+    # Fall back to first created compatible profile
+    first = profiles[0]
+    return {"profile_id": str(first.id), "profile_name": first.name}
+
+
+# ---------------------------------------------------------------------------
+# Default profile management
+# ---------------------------------------------------------------------------
+
+
+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():
+        try:
+            profile_uuid = uuid.UUID(profile_id_str)
+        except ValueError:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail=f"Invalid profile ID for tool type {tool_type_id}: {profile_id_str}",
+            )
+        profile = await session.get(ConfigProfile, profile_uuid)
+        if profile is None:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Profile not found: {profile_id_str}",
+            )
+        if profile.user_id != user_id:
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail=f"Profile does not belong to user: {profile_id_str}",
+            )
+
+
+@router.get("/defaults")
+async def get_default_profiles_endpoint(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all default profile mappings for the current 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 {}}
+
+
+@router.put("/defaults")
+async def set_default_profiles_endpoint(
+    data: DefaultProfilesUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Set default profile mappings for the current user."""
+    await _validate_default_profiles(session, user_id, data.default_profiles)
+    user_config = await _get_or_create_user_config(session, user_id)
+    user_config.config = {
+        **user_config.config,
+        "default_profiles": data.default_profiles,
+    }
+    await session.commit()
+    await session.refresh(user_config)
+    return {"default_profiles": user_config.default_profiles}
+
+
+@router.get("/defaults/{tool_type_id}")
+async def get_default_profile_for_tool_type_endpoint(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get the default profile ID 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}
+
+
+@router.post("/validate-git-url", response_model=ValidateGitUrlResponse)
+async def validate_git_url(
+    data: ValidateGitUrlRequest,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ValidateGitUrlResponse:
+    """Validate a git remote URL and list available branches.
+
+    Parses the URL, suggests corrections for browser URLs, and runs
+    git ls-remote to verify reachability and enumerate branches.
+    """
+    parse_result = parse_git_url(data.url)
+    original_url = data.url.strip()
+    url_to_check = parse_result.get("base_url") or original_url
+
+    if not url_to_check:
+        return ValidateGitUrlResponse(
+            valid=False,
+            error=parse_result.get("message", "Invalid URL"),
+            error_code=parse_result.get("error_code", "INVALID_URL"),
+        )
+
+    # If the URL needed parsing, return suggestion without checking remote
+    if parse_result.get("needs_parsing") and url_to_check != original_url:
+        return ValidateGitUrlResponse(
+            valid=False,
+            suggested_url=url_to_check,
+            error=parse_result.get("message"),
+            error_code=parse_result.get("error_code", "URL_NEEDS_PARSING"),
+        )
+
+    # Optional SSH key for private repos
+    env = None
+    key_path = None
+    if data.ssh_key_id:
+        from src.models import SSHKey
+        from src.services.shared.ssh_keys import _get_fernet
+
+        try:
+            ssh_key_uuid = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            return ValidateGitUrlResponse(
+                valid=False,
+                error="Invalid SSH key ID format",
+                error_code="INVALID_SSH_KEY",
+            )
+
+        ssh_key = await session.get(SSHKey, ssh_key_uuid)
+        if ssh_key is None or ssh_key.user_id != current_user_id:
+            return ValidateGitUrlResponse(
+                valid=False,
+                error="SSH key not found or not authorized",
+                error_code="SSH_KEY_NOT_FOUND",
+            )
+
+        import tempfile
+
+        fernet = _get_fernet()
+        private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+        fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
+        try:
+            os.write(fd, private_key.encode())
+        finally:
+            os.close(fd)
+        os.chmod(key_path, 0o600)
+        env = {
+            "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
+        }
+
+    try:
+        result = subprocess.run(
+            ["git", "ls-remote", "--heads", url_to_check],
+            capture_output=True,
+            text=True,
+            timeout=30,
+            env={**os.environ, **env} if env else None,
+        )
+    except subprocess.TimeoutExpired:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="Remote repository check timed out",
+            error_code="TIMEOUT",
+        )
+    except FileNotFoundError:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="git command not found on server",
+            error_code="GIT_NOT_FOUND",
+        )
+    finally:
+        if key_path and os.path.exists(key_path):
+            os.unlink(key_path)
+
+    if result.returncode != 0:
+        stderr = result.stderr.strip()
+        if (
+            "could not resolve" in stderr.lower()
+            or "unable to access" in stderr.lower()
+        ):
+            error_msg = "Could not reach repository. Check the URL and network access."
+            error_code = "UNREACHABLE"
+        elif (
+            "authentication" in stderr.lower() or "permission denied" in stderr.lower()
+        ):
+            error_msg = (
+                "Authentication failed. Provide an SSH key for private repositories."
+            )
+            error_code = "AUTH_FAILED"
+        else:
+            error_msg = f"Repository not accessible: {stderr[:200]}"
+            error_code = "REMOTE_ERROR"
+        return ValidateGitUrlResponse(
+            valid=False,
+            error=error_msg,
+            error_code=error_code,
+        )
+
+    # Parse branches from ls-remote output
+    branches: list[str] = []
+    default_branch = "main"
+    for line in result.stdout.strip().split("\n"):
+        if not line.strip():
+            continue
+        parts = line.split()
+        if len(parts) == 2:
+            ref = parts[1]
+            # refs/heads/branch-name
+            if ref.startswith("refs/heads/"):
+                branch_name = ref[len("refs/heads/") :]
+                branches.append(branch_name)
+                if branch_name in ("main", "master"):
+                    default_branch = branch_name
+
+    if not branches:
+        return ValidateGitUrlResponse(
+            valid=False,
+            error="No branches found in remote repository",
+            error_code="NO_BRANCHES",
+        )
+
+    return ValidateGitUrlResponse(
+        valid=True,
+        suggested_url=url_to_check if url_to_check != original_url else None,
+        branches=branches,
+        default_branch=default_branch,
+    )

apps/api/src/api/config/user_config.py

@@ -0,0 +1,98 @@
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends
+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.models import UserConfig
+from src.schemas.user 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
+) -> UserConfig:
+    """Get or create user config record.
+
+    Args:
+        session: Database session.
+        user_id: UUID of the user.
+
+    Returns:
+        The user's config, creating a new one if it doesn't exist.
+    """
+    result = await session.execute(
+        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={})
+        session.add(config)
+        await session.commit()
+        await session.refresh(config)
+    return config
+
+
+@router.get(
+    "/config",
+    response_model=UserConfigResponse,
+    summary="Get user config",
+    description="Get the current user's configuration settings.",
+)
+async def get_user_config(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> UserConfigResponse:
+    """Get the current user's configuration.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The user's configuration settings.
+    """
+    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user_id)
+    return UserConfigResponse.model_validate(config.config)
+
+
+@router.patch(
+    "/config",
+    response_model=UserConfigResponse,
+    summary="Update user config",
+    description="Update the current user's configuration settings.",
+)
+async def update_user_config(
+    data: UserConfigUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> UserConfigResponse:
+    """Update the current user's configuration.
+
+    Args:
+        data: Configuration update data with optional fields.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated user configuration.
+    """
+    _user = await _get_user(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)
+    # 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)
+    return UserConfigResponse.model_validate(config.config)

apps/api/src/api/git_repositories.py

@@ -1,799 +0,0 @@
-import os
-import shutil
-import subprocess
-import uuid
-from datetime import datetime
-
-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_current_user_id, get_db_session
-from src.config import Settings
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.user import User
-from src.utils.git_files import (
-    commit_file,
-    get_file_content,
-    list_branches,
-    list_tree,
-)
-from src.utils.git_control import (
-    checkout_branch,
-    commit_changes,
-    create_branch,
-    delete_branch,
-    fetch,
-    get_status,
-    merge,
-    pull,
-    push,
-)
-from src.utils.git_history import get_commit_detail, get_commit_history
-from src.utils.git_url_parser import parse_git_url
-
-router = APIRouter(prefix="/projects", tags=["git-repositories"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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,
-    session: AsyncSession,
-) -> Project:
-    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:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
-    return project
-
-
-def _get_repo_path(user_id: uuid.UUID, project_id: uuid.UUID, name: str) -> str:
-    base = Settings().repo_base_path or "/data/repos"
-    return os.path.join(base, str(user_id), str(project_id), f"{name}.git")
-
-
-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
-
-
-@router.get("/{project_id}/repositories", response_model=list[GitRepositoryResponse])
-async def list_repositories(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[GitRepository]:
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    result = await session.execute(
-        select(GitRepository).where(GitRepository.project_id == project_id)
-    )
-    return list(result.scalars().all())
-
-
-@router.delete("/{project_id}/repositories/{repo_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> Response:
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    # Remove from disk
-    if os.path.exists(repo.path):
-        shutil.rmtree(repo.path)
-
-    await session.delete(repo)
-    await session.commit()
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.post("/repositories/parse-url", response_model=URLParseResponse)
-async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
-    """Parse a git URL and detect if it's a browser URL that needs correction."""
-    result = parse_git_url(data.url)
-    return URLParseResponse(**result)
-
-
-@router.post("/{project_id}/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
-async def create_repository(
-    project_id: uuid.UUID,
-    data: GitRepositoryCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> GitRepository:
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    # Check for duplicate name
-    existing = await session.execute(
-        select(GitRepository).where(
-            GitRepository.project_id == project_id,
-            GitRepository.name == data.name,
-        )
-    )
-    if existing.scalar_one_or_none():
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
-
-    # Validate and potentially correct the URL
-    remote_url = data.remote_url
-    if remote_url and not data.force_original_url:
-        parse_result = parse_git_url(remote_url)
-        if parse_result["needs_parsing"] and parse_result["base_url"]:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail={
-                    "message": "The provided URL appears to be a browser URL, not a git clone URL",
-                    "suggested_url": parse_result["base_url"],
-                    "original_url": remote_url,
-                    "error_code": "URL_NEEDS_PARSING",
-                },
-            )
-        # Use base_url if it was extracted (for URLs without .git suffix)
-        if parse_result["base_url"]:
-            remote_url = parse_result["base_url"]
-
-    repo_path = _get_repo_path(user_id, project_id, data.name)
-
-    # Ensure parent directory exists
-    os.makedirs(os.path.dirname(repo_path), exist_ok=True)
-
-    if remote_url:
-        # Clone as mirror
-        try:
-            result = subprocess.run(
-                ["git", "clone", "--mirror", remote_url, repo_path],
-                capture_output=True,
-                text=True,
-                timeout=300,
-            )
-            if result.returncode != 0:
-                raise HTTPException(
-                    status_code=status.HTTP_400_BAD_REQUEST,
-                    detail=f"failed to clone repository: {result.stderr}",
-                )
-        except subprocess.TimeoutExpired:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="clone operation timed out")
-        except FileNotFoundError:
-            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
-    else:
-        # Init bare repo
-        try:
-            result = subprocess.run(
-                ["git", "init", "--bare", repo_path],
-                capture_output=True,
-                text=True,
-                check=True,
-            )
-        except FileNotFoundError:
-            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
-
-    repo = GitRepository(
-        name=data.name,
-        path=repo_path,
-        project_id=project_id,
-        owner_id=user_id,
-        is_mirror=bool(remote_url),
-        remote_url=remote_url,
-    )
-    session.add(repo)
-    await session.commit()
-    await session.refresh(repo)
-    return repo
-
-
-@router.get("/{project_id}/repositories/{repo_id}/history")
-async def get_repository_history(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    view: str = "graph",
-    branch: str | None = None,
-    limit: int = 100,
-    offset: int = 0,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get commit history for a repository."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        history = get_commit_history(repo.path, branch=branch, limit=limit, offset=offset)
-        return history
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e))
-
-
-@router.get("/{project_id}/repositories/{repo_id}/commits/{commit_hash}")
-async def get_repository_commit(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    commit_hash: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get detailed information about a specific commit."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        detail = get_commit_detail(repo.path, commit_hash)
-        return detail
-    except (RuntimeError, ValueError) as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-# File browsing endpoints
-
-
-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
-
-
-@router.get("/{project_id}/repositories/{repo_id}/files", response_model=FileListResponse)
-async def list_repository_files(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str = "main",
-    path: str = "",
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileListResponse:
-    """List files and directories in a repository path."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        entries = list_tree(repo.path, branch=branch, path=path)
-        return FileListResponse(
-            path=path,
-            branch=branch,
-            entries=[
-                {
-                    "name": e.name,
-                    "type": e.type,
-                    "path": e.path,
-                    "size": e.size,
-                    "mode": e.mode,
-                    "last_commit": e.last_commit,
-                }
-                for e in entries
-            ],
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-@router.get("/{project_id}/repositories/{repo_id}/files/content", response_model=FileContentResponse)
-async def get_repository_file_content(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str,
-    path: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileContentResponse:
-    """Get the content of a file."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        file_content = get_file_content(repo.path, branch=branch, path=path)
-        return FileContentResponse(
-            path=file_content.path,
-            branch=file_content.branch,
-            content=file_content.content,
-            size=file_content.size,
-            encoding=file_content.encoding,
-            language=file_content.language,
-            is_binary=file_content.is_binary,
-            last_commit=file_content.last_commit,
-        )
-    except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-@router.get("/{project_id}/repositories/{repo_id}/branches", response_model=BranchesResponse)
-async def get_repository_branches(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> BranchesResponse:
-    """List all branches in the repository."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        branches, default_branch = list_branches(repo.path)
-        return BranchesResponse(
-            branches=[
-                {
-                    "name": b.name,
-                    "is_default": b.is_default,
-                    "last_commit": b.last_commit,
-                }
-                for b in branches
-            ],
-            default_branch=default_branch,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-@router.post("/{project_id}/repositories/{repo_id}/files/content", response_model=FileUpdateResponse)
-async def update_repository_file(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: FileUpdateRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileUpdateResponse:
-    """Update a file and create a commit."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    # Get user info for commit
-    user = await _get_user(session, user_id)
-    author_name = user.name or "Unknown"
-    author_email = user.email or "unknown@example.com"
-
-    try:
-        commit_hash = commit_file(
-            repo_path=repo.path,
-            branch=data.branch,
-            path=data.path,
-            content=data.content,
-            commit_message=data.commit_message,
-            author_name=author_name,
-            author_email=author_email,
-        )
-        return FileUpdateResponse(
-            commit_hash=commit_hash,
-            message=data.commit_message,
-            branch=data.branch,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-# Git Control Endpoints
-
-
-class StatusResponse(BaseModel):
-    branch: str
-    modified: list[str]
-    added: list[str]
-    deleted: list[str]
-    untracked: list[str]
-    renamed: list[str]
-    ahead: int
-    behind: int
-
-
-@router.get("/{project_id}/repositories/{repo_id}/status", response_model=StatusResponse)
-async def get_repository_status(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> StatusResponse:
-    """Get the working directory status."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        status_result = get_status(repo.path)
-        return StatusResponse(
-            branch=status_result.branch,
-            modified=status_result.modified,
-            added=status_result.added,
-            deleted=status_result.deleted,
-            untracked=status_result.untracked,
-            renamed=status_result.renamed,
-            ahead=status_result.ahead,
-            behind=status_result.behind,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class BranchCreateRequest(BaseModel):
-    name: str
-    base_branch: str = "HEAD"
-
-
-class CheckoutRequest(BaseModel):
-    branch: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/branches")
-async def create_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: BranchCreateRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new branch."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        create_branch(repo.path, data.name, data.base_branch)
-        return {"message": f"Branch '{data.name}' created", "branch": data.name}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-@router.delete("/{project_id}/repositories/{repo_id}/branches/{branch_name}")
-async def delete_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch_name: str,
-    force: bool = False,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Delete a branch."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        delete_branch(repo.path, branch_name, force)
-        return {"message": f"Branch '{branch_name}' deleted"}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-@router.post("/{project_id}/repositories/{repo_id}/checkout")
-async def checkout_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CheckoutRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Checkout a branch."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        checkout_branch(repo.path, data.branch)
-        return {"message": f"Checked out branch '{data.branch}'", "branch": data.branch}
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class CommitRequest(BaseModel):
-    message: str
-    files: list[str] | None = None
-
-
-class CommitResponse(BaseModel):
-    commit_hash: str
-    message: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/commit", response_model=CommitResponse)
-async def commit_repository_changes(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CommitRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> CommitResponse:
-    """Commit changes to the repository."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    # Get user info for commit
-    user = await _get_user(session, user_id)
-    author_name = user.name or "Unknown"
-    author_email = user.email or "unknown@example.com"
-
-    try:
-        commit_hash = commit_changes(
-            repo_path=repo.path,
-            message=data.message,
-            author_name=author_name,
-            author_email=author_email,
-            files=data.files,
-        )
-        return CommitResponse(
-            commit_hash=commit_hash,
-            message=data.message,
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class FetchResponse(BaseModel):
-    message: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/fetch", response_model=FetchResponse)
-async def fetch_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> FetchResponse:
-    """Fetch from remote."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        fetch(repo.path)
-        return FetchResponse(message="Fetched from remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class PullResponse(BaseModel):
-    message: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/pull", response_model=PullResponse)
-async def pull_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> PullResponse:
-    """Pull updates from remote."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        pull(repo.path, branch)
-        return PullResponse(message="Pulled from remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class PushResponse(BaseModel):
-    message: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/push", response_model=PushResponse)
-async def push_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    branch: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> PushResponse:
-    """Push changes to remote."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        push(repo.path, branch)
-        return PushResponse(message="Pushed to remote")
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
-
-
-class MergeRequest(BaseModel):
-    source_branch: str
-    target_branch: str | None = None
-    message: str | None = None
-
-
-class MergeResponse(BaseModel):
-    commit_hash: str
-    message: str
-
-
-@router.post("/{project_id}/repositories/{repo_id}/merge", response_model=MergeResponse)
-async def merge_repository_branches(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: MergeRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> MergeResponse:
-    """Merge branches."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
-
-    if not os.path.exists(repo.path):
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
-
-    try:
-        commit_hash = merge(
-            repo_path=repo.path,
-            source_branch=data.source_branch,
-            target_branch=data.target_branch,
-            message=data.message,
-        )
-        return MergeResponse(
-            commit_hash=commit_hash,
-            message=data.message or f"Merge {data.source_branch}",
-        )
-    except RuntimeError as e:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))

apps/api/src/api/project/__init__.py

@@ -0,0 +1,6 @@
+"""Project API routers module."""
+
+from src.api.project.git_repositories import router as git_repositories_router
+from src.api.project.projects import router as projects_router
+
+__all__ = ["git_repositories_router", "projects_router"]

apps/api/src/api/project/projects.py

@@ -0,0 +1,275 @@
+import os
+import shutil
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, Response, status
+from sqlalchemy import func, 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.models import GitRepository
+from src.models.project import Project
+from src.models import SSHKey
+from src.models import ToolInstance
+from src.schemas.project import (
+    ProjectCreate,
+    ProjectResponse,
+    ProjectUpdate,
+    SetDefaultSSHKeyRequest,
+)
+
+router = APIRouter(prefix="/projects", tags=["projects"])
+
+
+@router.post(
+    "",
+    response_model=ProjectResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create a new project",
+    description="Create a new project for the authenticated user.",
+)
+async def create_project(
+    data: ProjectCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Project:
+    """Create a new project.
+
+    Args:
+        data: Project creation data including name and optional description.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The newly created project.
+    """
+    user = await _get_user(session, user_id)
+    project = Project(
+        name=data.name,
+        description=data.description,
+        owner_id=user.id,
+        default_ssh_key_id=None,
+    )
+    session.add(project)
+    await session.commit()
+    await session.refresh(project)
+    return project
+
+
+@router.get(
+    "",
+    summary="List all projects",
+    description="Retrieve all projects owned by the authenticated user with repositories and workspaces.",
+)
+async def list_projects(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[dict]:
+    """List all projects for the authenticated user.
+
+    Returns projects with nested repositories and workspaces for inline display.
+    """
+    user = await _get_user(session, user_id)
+    result = await session.execute(
+        select(Project)
+        .where(Project.owner_id == user.id)
+        .order_by(Project.created_at.desc())
+    )
+    projects = result.scalars().all()
+
+    from src.models import Workspace
+
+    enriched = []
+    for project in projects:
+        repos_result = await session.execute(
+            select(GitRepository).where(GitRepository.project_id == project.id)
+        )
+        repositories = []
+        for repo in repos_result.scalars().all():
+            ws_result = await session.execute(
+                select(Workspace).where(Workspace.repo_id == repo.id)
+            )
+            workspaces = []
+            for ws in ws_result.scalars().all():
+                # Count instances
+                inst_result = await session.execute(
+                    select(func.count()).where(ToolInstance.workspace_id == ws.id)
+                )
+                instance_count = inst_result.scalar() or 0
+                workspaces.append(
+                    {
+                        "id": str(ws.id),
+                        "name": ws.name,
+                        "branch": ws.branch,
+                        "status": ws.status,
+                        "instance_count": instance_count,
+                    }
+                )
+
+            repositories.append(
+                {
+                    "id": str(repo.id),
+                    "name": repo.name,
+                    "remote_url": repo.remote_url,
+                    "workspaces": workspaces,
+                }
+            )
+
+        enriched.append(
+            {
+                "id": str(project.id),
+                "name": project.name,
+                "description": project.description,
+                "owner_id": str(project.owner_id),
+                "repositories": repositories,
+                "created_at": project.created_at.isoformat()
+                if project.created_at
+                else None,
+            }
+        )
+
+    return enriched
+
+
+@router.get(
+    "/{project_id}",
+    response_model=ProjectResponse,
+    summary="Get a project",
+    description="Retrieve a specific project by ID.",
+)
+async def get_project(
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Project:
+    """Get a specific project by ID.
+
+    Args:
+        project_id: UUID of the project to retrieve.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The requested project.
+    """
+    await _get_user(session, user_id)
+    return await _get_owned_project(project_id, user_id, session)
+
+
+@router.patch(
+    "/{project_id}",
+    response_model=ProjectResponse,
+    summary="Update a project",
+    description="Update a project's name or description.",
+)
+async def update_project(
+    project_id: uuid.UUID,
+    data: ProjectUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Project:
+    """Update a project.
+
+    Args:
+        project_id: UUID of the project to update.
+        data: Project update data with optional name and description.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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
+    if data.description is not None:
+        project.description = data.description
+
+    await session.commit()
+    await session.refresh(project)
+    return project
+
+
+@router.delete(
+    "/{project_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete a project",
+    description="Delete a project and all its associated repositories.",
+)
+async def delete_project(
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Response:
+    """Delete a project and all its repositories.
+
+    Args:
+        project_id: UUID of the project to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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)
+    )
+    repositories = result.scalars().all()
+    for repo in repositories:
+        if os.path.exists(repo.path):
+            shutil.rmtree(repo.path)
+        await session.delete(repo)
+
+    await session.delete(project)
+    await session.commit()
+    return Response(status_code=status.HTTP_204_NO_CONTENT)
+
+
+@router.patch(
+    "/{project_id}/default-ssh-key",
+    response_model=ProjectResponse,
+    summary="Set default SSH key",
+    description="Set the default SSH key for a project.",
+)
+async def set_default_ssh_key(
+    project_id: uuid.UUID,
+    data: SetDefaultSSHKeyRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Project:
+    """Set the default SSH key for a project.
+
+    Args:
+        project_id: UUID of the project.
+        data: Request containing the SSH key ID to set as default.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="invalid ssh key",
+        )
+
+    project.default_ssh_key_id = data.ssh_key_id
+    await session.commit()
+    await session.refresh(project)
+    return project

apps/api/src/api/projects.py

@@ -1,164 +0,0 @@
-import os
-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_current_user_id, get_db_session
-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
-
-router = APIRouter(prefix="/projects", tags=["projects"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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
-
-
-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("", response_model=ProjectResponse, status_code=status.HTTP_201_CREATED)
-async def create_project(
-    data: ProjectCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> Project:
-    user = await _get_user(session, user_id)
-    project = Project(
-        name=data.name,
-        description=data.description,
-        owner_id=user.id,
-        default_ssh_key_id=None,
-    )
-    session.add(project)
-    await session.commit()
-    await session.refresh(project)
-    return project
-
-
-@router.get("", response_model=list[ProjectResponse])
-async def list_projects(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[Project]:
-    user = await _get_user(session, user_id)
-    result = await session.execute(select(Project).where(Project.owner_id == user.id))
-    return list(result.scalars().all())
-
-
-@router.get("/{project_id}", response_model=ProjectResponse)
-async def get_project(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> Project:
-    await _get_user(session, user_id)
-    return await _get_owned_project(project_id, user_id, session)
-
-
-async def _get_owned_project(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID,
-    session: AsyncSession,
-) -> Project:
-    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:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
-    return project
-
-
-@router.patch("/{project_id}", response_model=ProjectResponse)
-async def update_project(
-    project_id: uuid.UUID,
-    data: ProjectUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> 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
-    if data.description is not None:
-        project.description = data.description
-
-    await session.commit()
-    await session.refresh(project)
-    return project
-
-
-@router.delete("/{project_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_project(
-    project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> Response:
-    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))
-    repositories = result.scalars().all()
-    for repo in repositories:
-        if os.path.exists(repo.path):
-            shutil.rmtree(repo.path)
-        await session.delete(repo)
-
-    await session.delete(project)
-    await session.commit()
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.patch("/{project_id}/default-ssh-key", response_model=ProjectResponse)
-async def set_default_ssh_key(
-    project_id: uuid.UUID,
-    data: SetDefaultSSHKeyRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> 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:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="invalid ssh key",
-        )
-
-    project.default_ssh_key_id = data.ssh_key_id
-    await session.commit()
-    await session.refresh(project)
-    return project

apps/api/src/api/shared_validators.py

@@ -0,0 +1,98 @@
+"""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

@@ -1,117 +0,0 @@
-import uuid
-from datetime import datetime
-
-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_current_user_id, get_db_session
-from src.config import Settings
-from src.models.ssh_key import SSHKey
-from src.models.user import User
-
-router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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
-
-
-def _get_fernet() -> Fernet:
-    """Generate a valid Fernet key from the session secret."""
-    import base64
-    import hashlib
-    
-    settings = Settings()
-    # Derive a 32-byte key from the session secret using SHA256
-    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
-    # Base64 encode it for Fernet (must be 32 url-safe base64-encoded bytes)
-    key = base64.urlsafe_b64encode(key_bytes)
-    return Fernet(key)
-
-
-def generate_ssh_key_pair() -> tuple[str, str]:
-    private_key = Ed25519PrivateKey.generate()
-    public_key = private_key.public_key()
-
-    private_bytes = private_key.private_bytes(
-        encoding=serialization.Encoding.PEM,
-        format=serialization.PrivateFormat.OpenSSH,
-        encryption_algorithm=serialization.NoEncryption(),
-    )
-
-    public_bytes = public_key.public_bytes(
-        encoding=serialization.Encoding.OpenSSH,
-        format=serialization.PublicFormat.OpenSSH,
-    )
-
-    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
-
-
-@router.post("", response_model=SSHKeyResponse, status_code=status.HTTP_201_CREATED)
-async def create_ssh_key(
-    data: SSHKeyCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> SSHKey:
-    user = await _get_user(session, user_id)
-    private_key, public_key = generate_ssh_key_pair()
-
-    fernet = _get_fernet()
-    encrypted_private = fernet.encrypt(private_key.encode()).decode()
-
-    ssh_key = SSHKey(
-        name=data.name,
-        public_key=public_key,
-        private_key_encrypted=encrypted_private,
-        user_id=user.id,
-    )
-    session.add(ssh_key)
-    await session.commit()
-    await session.refresh(ssh_key)
-    return ssh_key
-
-
-@router.get("", response_model=list[SSHKeyResponse])
-async def list_ssh_keys(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[SSHKey]:
-    user = await _get_user(session, user_id)
-    result = await session.execute(select(SSHKey).where(SSHKey.user_id == user.id))
-    return list(result.scalars().all())
-
-
-@router.delete("/{key_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_ssh_key(
-    key_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    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()

apps/api/src/api/system/__init__.py

@@ -0,0 +1,17 @@
+"""System API routers module."""
+
+from src.api.system.dashboard import router as dashboard_router
+from src.api.system.events import router as events_router
+from src.api.system.health import router as health_router
+from src.api.system.instance_proxy import router as instance_proxy_router
+from src.api.system.notifications import router as notifications_router
+from src.api.system.terminal import router as terminal_router
+
+__all__ = [
+    "dashboard_router",
+    "events_router",
+    "health_router",
+    "instance_proxy_router",
+    "notifications_router",
+    "terminal_router",
+]

apps/api/src/api/system/dashboard.py

@@ -5,18 +5,31 @@ from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 
 router = APIRouter(prefix="/dashboard", tags=["dashboard"])
 
 
-@router.get("/summary")
+@router.get(
+    "/summary",
+    summary="Get dashboard summary",
+    description="Get a summary of the user's projects, repositories, SSH keys, and recent activity.",
+)
 async def get_dashboard_summary(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
+    """Get a summary of the user's dashboard data.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Dictionary with counts of projects, repositories, SSH keys, and recent activity.
+    """
     # Count user's projects
     projects_result = await session.execute(
         select(func.count()).select_from(Project).where(Project.owner_id == user_id)

apps/api/src/api/system/events.py

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

apps/api/src/api/system/health.py

@@ -0,0 +1,115 @@
+"""Health check endpoints and models."""
+
+import time
+from datetime import datetime, timezone
+from typing import Any
+
+from fastapi import APIRouter
+from sqlalchemy import text
+
+from src.database import SessionLocal
+from src.schemas.system import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
+
+router = APIRouter()
+
+# Track start time for uptime
+_start_time = time.time()
+
+
+@router.get(
+    "/health",
+    response_model=HealthResponse,
+    summary="Health check",
+    description="Returns overall system health status including database and disk checks.",
+    tags=["Health"],
+)
+async def health_check() -> dict[str, Any]:
+    """Check overall system health.
+
+    Returns:
+        HealthResponse with status, timestamp, version, checks, and uptime.
+    """
+    checks = HealthChecks()
+    overall_status = "healthy"
+
+    # Database check
+    try:
+        import time as time_module
+
+        start = time_module.perf_counter()
+        async with SessionLocal() as session:
+            await session.execute(text("SELECT 1"))
+        db_time = (time_module.perf_counter() - start) * 1000
+        checks.database = DatabaseHealth(
+            status="healthy",
+            response_time_ms=round(db_time, 2),
+        )
+    except Exception:
+        checks.database = DatabaseHealth(
+            status="unhealthy",
+            response_time_ms=0.0,
+        )
+        overall_status = "degraded"
+
+    # Disk check
+    try:
+        import shutil
+
+        disk = shutil.disk_usage("/")
+        free_gb = disk.free / (1024**3)
+        total_gb = disk.total / (1024**3)
+        disk_status = "healthy" if free_gb > 1.0 else "degraded"
+        if disk_status == "degraded":
+            overall_status = "degraded"
+        checks.disk = DiskHealth(
+            status=disk_status,
+            free_gb=round(free_gb, 2),
+            total_gb=round(total_gb, 2),
+        )
+    except Exception:
+        checks.disk = None
+
+    return HealthResponse(
+        status=overall_status,
+        timestamp=datetime.now(timezone.utc).isoformat().replace("+00:00", "Z"),
+        version="0.1.0",
+        checks=checks,
+        uptime_seconds=round(time.time() - _start_time, 2),
+    ).model_dump()
+
+
+@router.get(
+    "/health/db",
+    response_model=DatabaseHealthResponse,
+    summary="Database health check",
+    description="Returns database-specific health status with response time.",
+    tags=["Health"],
+)
+async def health_check_db() -> dict[str, Any]:
+    """Check database health.
+
+    Returns:
+        DatabaseHealthResponse with status and response time.
+    """
+    import time as time_module
+
+    try:
+        start = time_module.perf_counter()
+        async with SessionLocal() as session:
+            await session.execute(text("SELECT 1"))
+        db_time = (time_module.perf_counter() - start) * 1000
+        return DatabaseHealthResponse(
+            status="healthy",
+            response_time_ms=round(db_time, 2),
+        ).model_dump()
+    except Exception:
+        return DatabaseHealthResponse(
+            status="unhealthy",
+            response_time_ms=0.0,
+        ).model_dump()

apps/api/src/api/system/instance_proxy.py

@@ -0,0 +1,124 @@
+"""Instance proxy router for forwarding HTTP requests to running containers."""
+
+import logging
+import uuid
+
+import httpx
+from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models import ToolInstance
+from src.models import ToolType
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/instances", tags=["instance-proxy"])
+
+
+async def _proxy_request(
+    request: Request,
+    instance_id: uuid.UUID,
+    path: str,
+    user_id: uuid.UUID,
+    session: AsyncSession,
+) -> Response:
+    """Proxy an HTTP request to a running instance."""
+    instance = await session.get(ToolInstance, instance_id)
+    if instance is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
+        )
+
+    # Verify ownership
+    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_name:
+        raise HTTPException(
+            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
+            detail="instance is not running",
+        )
+
+    # Get the tool type to find the internal port
+    tool_type = await session.get(ToolType, instance.tool_type_id)
+    internal_port = tool_type.default_port if tool_type and tool_type.default_port else instance.port
+
+    # Build target URL using internal port
+    target_url = f"http://{instance.container_name}:{internal_port}"
+    if path:
+        target_url += f"/{path}"
+
+    # Get query string
+    query_string = str(request.query_params)
+    if query_string:
+        target_url += f"?{query_string}"
+
+    # Forward headers (excluding host and cookies)
+    headers: dict[str, str] = {}
+    for key, value in request.headers.items():
+        if key.lower() not in ("host", "cookie", "content-length"):
+            headers[key] = value
+
+    # Forward the request
+    try:
+        async with httpx.AsyncClient() as client:
+            body = await request.body()
+            response = await client.request(
+                method=request.method,
+                url=target_url,
+                headers=headers,
+                content=body,
+                follow_redirects=False,
+                timeout=30.0,
+            )
+    except Exception as exc:
+        logger.error("Proxy error to %s: %s", target_url, exc)
+        raise HTTPException(
+            status_code=status.HTTP_502_BAD_GATEWAY,
+            detail=f"failed to reach instance: {exc}",
+        )
+
+    # Build response
+    response_headers = dict(response.headers)
+    # Remove hop-by-hop headers
+    for header in ("content-encoding", "transfer-encoding", "connection"):
+        response_headers.pop(header, None)
+
+    return Response(
+        content=response.content,
+        status_code=response.status_code,
+        headers=response_headers,
+    )
+
+
+@router.get("/{instance_id}/proxy/{path:path}")
+@router.post("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.put("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.delete("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.patch("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.head("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+@router.options("/{instance_id}/proxy/{path:path}", include_in_schema=False)
+async def proxy_to_instance(
+    request: Request,
+    instance_id: uuid.UUID,
+    path: str = "",
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Response:
+    """Proxy requests to a running tool instance.
+
+    Args:
+        request: The incoming HTTP request.
+        instance_id: UUID of the instance.
+        path: The path to proxy to the instance.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Response from the proxied instance.
+    """
+    return await _proxy_request(request, instance_id, path, user_id, session)

apps/api/src/api/system/notifications.py

@@ -0,0 +1,161 @@
+"""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 import UserConfig
+from src.services.shared.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/system/terminal.py

@@ -0,0 +1,749 @@
+"""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 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.models import TerminalSessionModel
+from src.models import ToolInstance
+from src.models import ToolType
+from src.services.terminal.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(
+    websocket: WebSocket,
+    instance_id: str,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """WebSocket endpoint for terminal access (default session alias).
+
+    Backward-compatible route that maps to the default session.
+    """
+    await _handle_terminal_websocket(websocket, instance_id, None, db_session)
+
+
+@router.websocket(
+    "/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.
+    """
+    logger.debug(
+        "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
+        )
+        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)
+        await websocket.close(code=4004, reason="Instance not found")
+        return
+
+    if instance.owner_id != user_id:
+        logger.warning(
+            "Forbidden terminal access for instance %s by user %s",
+            instance_id,
+            user_id,
+        )
+        await websocket.close(code=4003, reason="Forbidden")
+        return
+
+    if instance.status != "running" or not instance.container_id:
+        logger.warning(
+            "Instance %s not running (status=%s, container_id=%s)",
+            instance_id,
+            instance.status,
+            instance.container_id,
+        )
+        await websocket.close(code=4004, reason="Instance not running")
+        return
+
+    logger.debug("Terminal auth passed for instance %s, user %s", instance_id, user_id)
+
+    # Verify the container actually exists (may have been removed/recreated)
+    from src.services.docker import get_container_status
+
+    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:
+            # Default session alias
+            session = await terminal_manager.get_or_create_session(
+                instance_uuid,
+                instance.container_id,
+                startup_command=startup_command,
+            )
+            slot_session_id = "default"
+        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
+        session_ref = SessionRef(session, slot_session_id)
+
+        # Start write loop and heartbeat (read is now event-driven in TerminalSession)
+        write_task = asyncio.create_task(
+            _write_loop(session_ref, websocket, instance_id)
+        )
+        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(
+            [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
+                )
+
+
+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 == "ack":
+                                char_count = ctrl.get("chars", 0)
+                                if char_count > 0:
+                                    session.acknowledge_data(char_count)
+                            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,
+) -> uuid.UUID | None:
+    """Extract and validate user ID from session cookie in WebSocket.
+
+    Args:
+        websocket: The WebSocket connection.
+        db_session: Database session.
+
+    Returns:
+        The user's UUID if authenticated, None otherwise.
+    """
+    from src.auth.session import decode_session_cookie
+    from src.config import Settings
+
+    session_cookie = websocket.cookies.get("session")
+    if not session_cookie:
+        return None
+
+    settings = Settings()
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        return uuid.UUID(str(payload["user_id"]))
+    except (ValueError, KeyError):
+        return None

apps/api/src/api/tool/__init__.py

@@ -0,0 +1,13 @@
+"""Tool API routers module."""
+
+from src.api.tool.sessions import sessions_router
+from src.api.tool.tool_definitions import router as tool_definitions_router
+from src.api.tool.tool_instances import router as tool_instances_router
+from src.api.tool.tool_types import router as tool_types_router
+
+__all__ = [
+    "sessions_router",
+    "tool_definitions_router",
+    "tool_instances_router",
+    "tool_types_router",
+]

apps/api/src/api/tool/sessions.py

@@ -0,0 +1,80 @@
+"""Sessions API endpoints (running instances for current user)."""
+
+import uuid
+
+from fastapi import APIRouter, Depends
+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.models import GitRepository
+from src.models import Project
+from src.models import ToolInstance
+from src.models import ToolType
+
+sessions_router = APIRouter(prefix="/users", tags=["sessions"])
+
+
+@sessions_router.get(
+    "/me/sessions",
+    summary="Get user sessions",
+    description="Get all active sessions (running instances) for the current user.",
+)
+async def get_user_sessions(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all active sessions for the current user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Dictionary containing list of active sessions with instance details.
+    """
+    _user = await _get_user(session, user_id)
+
+    result = await session.execute(
+        select(ToolInstance)
+        .where(ToolInstance.owner_id == user_id)
+        .where(
+            ToolInstance.status.in_(
+                ["running", "building", "pending", "stopped", "error"]
+            )
+        )
+        .order_by(ToolInstance.created_at.desc())
+    )
+    instances = result.scalars().all()
+
+    sessions = []
+    for instance in instances:
+        tool_type = await session.get(ToolType, instance.tool_type_id)
+        repo = await session.get(GitRepository, instance.repository_id)
+        project = await session.get(Project, instance.project_id)
+
+        sessions.append(
+            {
+                "id": str(instance.id),
+                "display_name": instance.display_name,
+                "tool_type_name": tool_type.name if tool_type else "unknown",
+                "tool_icon": tool_type.name if tool_type else "code",
+                "tool_type_interfaces": [tool_type.interface_type] if tool_type else [],
+                "repository_name": repo.name if repo else "unknown",
+                "repository_id": str(instance.repository_id),
+                "project_name": project.name if project else "unknown",
+                "project_id": str(instance.project_id),
+                "status": instance.status,
+                "url": instance.url,
+                "clone_mode": instance.clone_mode,
+                "branch": instance.branch,
+                "selected_config_profile_id": str(instance.selected_config_profile_id)
+                if instance.selected_config_profile_id
+                else None,
+                "created_at": instance.created_at.isoformat()
+                if instance.created_at
+                else None,
+            }
+        )
+
+    return {"sessions": sessions}

apps/api/src/api/tool/tool_definitions.py

@@ -0,0 +1,424 @@
+"""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 import ToolDefinitionManifest
+from src.models import ToolType
+from src.services.build.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.is_(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/tool_types.py

@@ -0,0 +1,375 @@
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.api.tool.tool_types_validation import (
+    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 import ToolType
+from src.models.user import User
+from src.schemas.tool import (
+    ToolTypeCreate,
+    ToolTypeResponse,
+    ToolTypeUpdate,
+    ToolTypeValidateRequest,
+)
+
+router = APIRouter(prefix="/tool-types", tags=["tool-types"])
+
+
+async def _require_admin(user: User) -> None:
+    """Check if user has admin privileges.
+
+    For now, all authenticated users can manage tool types.
+    In production, this should check user.role or similar.
+    """
+    # For now, all authenticated users can manage tool types
+    # In production, check user.role or similar
+    pass
+
+
+@router.post(
+    "",
+    response_model=ToolTypeResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create tool type",
+    description="Create a new custom tool type with a Docker Compose template.",
+)
+async def create_tool_type(
+    data: ToolTypeCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ToolType:
+    """Create a new tool type.
+
+    Args:
+        data: Tool type creation data including name, display name, and compose template.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="tool type with this name already exists",
+        )
+
+    tool_type = ToolType(
+        name=data.name,
+        display_name=data.display_name,
+        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,
+        requires_port=data.requires_port,
+        created_by_id=user.id,
+    )
+    session.add(tool_type)
+    await session.commit()
+    await session.refresh(tool_type)
+    return tool_type
+
+
+@router.get(
+    "",
+    response_model=list[ToolTypeResponse],
+    summary="List tool types",
+    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),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[ToolType]:
+    """List all tool types.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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())
+
+
+@router.get(
+    "/{tool_type_id}",
+    response_model=ToolTypeResponse,
+    summary="Get tool type",
+    description="Get a specific tool type by ID.",
+)
+async def get_tool_type(
+    tool_type_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ToolType:
+    """Get a specific tool type by ID.
+
+    Args:
+        tool_type_id: UUID of the tool type to retrieve.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+    return tool_type
+
+
+@router.put(
+    "/{tool_type_id}",
+    response_model=ToolTypeResponse,
+    summary="Update tool type",
+    description="Update a custom tool type. Built-in tool types cannot be modified.",
+)
+async def update_tool_type(
+    tool_type_id: uuid.UUID,
+    data: ToolTypeUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ToolType:
+    """Update a tool type.
+
+    Args:
+        tool_type_id: UUID of the tool type to update.
+        data: Tool type update data with optional fields.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+
+    # Built-in tool types can now be modified
+
+    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 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",
+            )
+
+        # Only validate port exposure for compose definitions
+        definition_type = update_data.get("definition_type", tool_type.definition_type)
+        if definition_type == "compose":
+            template = update_data.get("compose_template", tool_type.compose_template)
+            if template:
+                try:
+                    parsed = validate_compose_yaml(template)
+                    if not check_port_exposed(parsed, new_port):
+                        raise HTTPException(
+                            status_code=status.HTTP_400_BAD_REQUEST,
+                            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(
+                update_data["compose_template"], update_data["required_variables"]
+            )
+        elif "required_variables" in update_data:
+            template = tool_type.compose_template
+            if template:
+                validate_required_variables(template, update_data["required_variables"])
+
+    # When switching to manifest, clear legacy templates
+    if definition_type == "manifest":
+        if "manifest_id" in update_data:
+            tool_type.manifest_id = update_data["manifest_id"]
+        tool_type.compose_template = None
+        tool_type.dockerfile_template = None
+
+    for field, value in update_data.items():
+        setattr(tool_type, field, value)
+
+    await session.commit()
+    await session.refresh(tool_type)
+    return tool_type
+
+
+@router.post(
+    "/validate",
+    summary="Validate tool type template",
+    description="Validate a compose template or dockerfile syntax before creating a tool type.",
+)
+async def validate_tool_type_template(
+    data: ToolTypeValidateRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Validate a tool type template syntax.
+
+    Args:
+        data: Validation request with definition type and template.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Validation result with success status and any errors.
+    """
+    await _get_user(session, user_id)
+
+    errors = []
+
+    if data.definition_type == "compose":
+        if not data.compose_template:
+            errors.append("Compose template is required")
+        else:
+            try:
+                validate_compose_yaml(data.compose_template)
+            except ValueError as e:
+                errors.append(str(e))
+
+    elif data.definition_type == "dockerfile":
+        if not data.dockerfile_template:
+            errors.append("Dockerfile template is required")
+        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'")
+
+    return {
+        "valid": len(errors) == 0,
+        "errors": errors,
+    }
+
+
+@router.get(
+    "/{tool_type_id}/validate",
+    summary="Validate tool type",
+    description="Validate the compose template or dockerfile syntax of a tool type.",
+)
+async def validate_tool_type(
+    tool_type_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Validate a tool type's template syntax.
+
+    Args:
+        tool_type_id: UUID of the tool type to validate.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+
+    errors = []
+
+    if tool_type.definition_type == "compose":
+        if not tool_type.compose_template:
+            errors.append("Compose template is empty")
+        else:
+            try:
+                validate_compose_yaml(tool_type.compose_template)
+            except ValueError as e:
+                errors.append(str(e))
+
+    elif tool_type.definition_type == "dockerfile":
+        if not tool_type.dockerfile_template:
+            errors.append("Dockerfile template is empty")
+        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,
+    }
+
+
+@router.delete(
+    "/{tool_type_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete tool type",
+    description="Delete a custom tool type. Built-in tool types cannot be deleted.",
+)
+async def delete_tool_type(
+    tool_type_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a tool type.
+
+    Args:
+        tool_type_id: UUID of the tool type to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+
+    # Built-in tool types can now be deleted
+
+    await session.delete(tool_type)
+    await session.commit()

apps/api/src/api/tool/tool_types_validation.py

@@ -0,0 +1,87 @@
+"""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/tool_instances.py

@@ -1,425 +0,0 @@
-"""Tool instance API endpoints."""
-
-import os
-import uuid
-from datetime import datetime
-
-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
-from src.database import get_db_session
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.services.docker import (
-    ensure_instance_directory,
-    execute_compose_command,
-    find_free_port,
-    get_container_id,
-    get_container_logs,
-    get_container_status,
-    render_compose_template,
-    write_compose_file,
-)
-
-router = APIRouter(prefix="/projects", tags=["tool-instances"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    user = await session.get(User, user_id)
-    if user is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="user not found"
-        )
-    return user
-
-
-async def _get_owned_project(
-    project_id: uuid.UUID, user_id: uuid.UUID, session: AsyncSession
-) -> Project:
-    project = await session.get(Project, project_id)
-    if project is None or project.owner_id != user_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="project not found"
-        )
-    return project
-
-
-@router.post("/{project_id}/repositories/{repo_id}/instances")
-async def create_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    tool_type_id: uuid.UUID,
-    display_name: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new tool instance for a repository."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found"
-        )
-
-    tool_type = await session.get(ToolType, tool_type_id)
-    if tool_type is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
-        )
-
-    # Generate unique name
-    instance_name = f"{tool_type.name}-{repo.name}-{uuid.uuid4().hex[:8]}"
-    instance_display = display_name or f"{tool_type.display_name} - {repo.name}"
-
-    # Create instance directory
-    instance_dir = ensure_instance_directory(instance_name)
-    compose_path = os.path.join(instance_dir, "docker-compose.yml")
-
-    # Find free port
-    tool_port = find_free_port()
-
-    # Render compose template
-    variables = {
-        "REPO_PATH": repo.path,
-        "INSTANCE_NAME": instance_name,
-        "INSTANCE_ID": instance_name,
-        "TOOL_PORT": tool_port,
-        "USER_ID": str(user_id),
-        "PROJECT_ID": str(project_id),
-    }
-    compose_content = render_compose_template(tool_type.compose_template, variables)
-    write_compose_file(instance_dir, compose_content)
-
-    # Create database record
-    instance = ToolInstance(
-        name=instance_name,
-        display_name=instance_display,
-        tool_type_id=tool_type_id,
-        repository_id=repo_id,
-        project_id=project_id,
-        owner_id=user_id,
-        status="pending",
-        compose_path=compose_path,
-        port=tool_port,
-    )
-    session.add(instance)
-    await session.commit()
-    await session.refresh(instance)
-
-    return {
-        "id": str(instance.id),
-        "name": instance.name,
-        "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id),
-        "status": instance.status,
-        "created_at": instance.created_at.isoformat(),
-    }
-
-
-@router.get("/{project_id}/repositories/{repo_id}/instances")
-async def list_instances(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List all instances for a repository."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    repo = await session.get(GitRepository, repo_id)
-    if repo is None or repo.project_id != project_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found"
-        )
-
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.repository_id == repo_id)
-        .where(ToolInstance.owner_id == user_id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    return {
-        "instances": [
-            {
-                "id": str(i.id),
-                "name": i.name,
-                "display_name": i.display_name,
-                "tool_type_id": str(i.tool_type_id),
-                "status": i.status,
-                "url": i.url,
-                "port": i.port,
-                "created_at": i.created_at.isoformat(),
-            }
-            for i in instances
-        ]
-    }
-
-
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def get_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a specific instance with real-time status."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    # Get real-time status from Docker
-    if instance.container_id:
-        docker_status = get_container_status(instance.container_id)
-        if docker_status == "running" and instance.status != "running":
-            instance.status = "running"
-            await session.commit()
-        elif docker_status == "exited" and instance.status == "running":
-            instance.status = "stopped"
-            instance.last_stopped_at = datetime.now()
-            await session.commit()
-
-    return {
-        "id": str(instance.id),
-        "name": instance.name,
-        "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id),
-        "status": instance.status,
-        "container_id": instance.container_id,
-        "compose_path": instance.compose_path,
-        "url": instance.url,
-        "port": instance.port,
-        "last_started_at": instance.last_started_at.isoformat() if instance.last_started_at else None,
-        "last_stopped_at": instance.last_stopped_at.isoformat() if instance.last_stopped_at else None,
-        "created_at": instance.created_at.isoformat(),
-    }
-
-
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/start")
-async def start_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Start a tool instance."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    if not instance.compose_path or not os.path.exists(instance.compose_path):
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST, detail="compose file not found"
-        )
-
-    instance.status = "building"
-    await session.commit()
-
-    # Execute docker compose up
-    returncode, stdout, stderr = execute_compose_command(
-        instance.compose_path, "up"
-    )
-
-    if returncode != 0:
-        instance.status = "error"
-        await session.commit()
-        raise HTTPException(
-            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"failed to start instance: {stderr}",
-        )
-
-    # Get container ID
-    container_id = get_container_id(instance.name)
-    if container_id:
-        instance.container_id = container_id
-
-    instance.status = "running"
-    instance.last_started_at = datetime.now()
-    instance.url = f"http://localhost:{instance.port}"
-    await session.commit()
-
-    return {"status": instance.status, "url": instance.url}
-
-
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/stop")
-async def stop_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Stop a tool instance."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    if instance.compose_path and os.path.exists(instance.compose_path):
-        execute_compose_command(instance.compose_path, "stop")
-
-    instance.status = "stopped"
-    instance.last_stopped_at = datetime.now()
-    instance.url = None
-    await session.commit()
-
-    return {"status": instance.status}
-
-
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/restart")
-async def restart_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Restart a tool instance."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    if instance.compose_path and os.path.exists(instance.compose_path):
-        returncode, stdout, stderr = execute_compose_command(
-            instance.compose_path, "restart"
-        )
-
-        if returncode == 0:
-            instance.status = "running"
-            instance.last_started_at = datetime.now()
-            instance.url = f"http://localhost:{instance.port}"
-            await session.commit()
-            return {"status": instance.status, "url": instance.url}
-
-    instance.status = "error"
-    await session.commit()
-    return {"status": instance.status}
-
-
-@router.delete("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def delete_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a tool instance."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    # Stop and remove container
-    if instance.compose_path and os.path.exists(instance.compose_path):
-        execute_compose_command(instance.compose_path, "down")
-
-    # Remove instance directory
-    if instance.compose_path:
-        instance_dir = os.path.dirname(instance.compose_path)
-        if os.path.exists(instance_dir):
-            import shutil
-            shutil.rmtree(instance_dir)
-
-    await session.delete(instance)
-    await session.commit()
-
-
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}/logs")
-async def get_instance_logs(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    tail: int = 100,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get container logs for an instance."""
-    _user = await _get_user(session, user_id)
-    _project = await _get_owned_project(project_id, user_id, session)
-
-    instance = await session.get(ToolInstance, instance_id)
-    if instance is None or instance.repository_id != repo_id:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
-        )
-
-    if not instance.container_id:
-        return {"logs": "No container running"}
-
-    logs = get_container_logs(instance.container_id, tail)
-    return {"logs": logs}
-
-
-from fastapi import APIRouter as FastAPIRouter
-
-sessions_router = FastAPIRouter(prefix="/users", tags=["sessions"])
-
-@sessions_router.get("/me/sessions")
-async def get_user_sessions(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get all active sessions (running instances) for the current user."""
-    _user = await _get_user(session, user_id)
-
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.owner_id == user_id)
-        .where(ToolInstance.status.in_(["running", "building", "pending"]))
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    sessions = []
-    for instance in instances:
-        tool_type = await session.get(ToolType, instance.tool_type_id)
-        repo = await session.get(GitRepository, instance.repository_id)
-        project = await session.get(Project, instance.project_id)
-
-        sessions.append({
-            "id": str(instance.id),
-            "display_name": instance.display_name,
-            "tool_type_name": tool_type.name if tool_type else "unknown",
-            "tool_icon": tool_type.name if tool_type else "code",
-            "repository_name": repo.name if repo else "unknown",
-            "project_name": project.name if project else "unknown",
-            "status": instance.status,
-            "url": instance.url,
-        })
-
-    return {"sessions": sessions}

apps/api/src/api/tool_types.py

@@ -1,237 +0,0 @@
-import uuid
-from datetime import datetime
-
-import yaml
-from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator
-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_type import ToolType
-from src.models.user import User
-
-router = APIRouter(prefix="/tool-types", tags=["tool-types"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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 _require_admin(user: User) -> None:
-    # For now, all authenticated users can manage tool types
-    # In production, check user.role or similar
-    pass
-
-
-class ToolTypeCreate(BaseModel):
-    name: str
-    display_name: str
-    description: str | None = None
-    compose_template: str
-    required_variables: list[str] = []
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str) -> str:
-        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("required_variables")
-    @classmethod
-    def validate_required_variables(cls, v: list[str], info) -> list[str]:
-        if not v:
-            return v
-        
-        # Get compose_template from the model data
-        data = info.data
-        if "compose_template" not in data:
-            return v
-        
-        template = data["compose_template"]
-        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
-
-
-class ToolTypeUpdate(BaseModel):
-    display_name: str | None = None
-    description: str | None = None
-    compose_template: str | None = None
-    required_variables: list[str] | None = None
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None) -> str | None:
-        if v is None:
-            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
-
-
-class ToolTypeResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    display_name: str
-    description: str | None
-    compose_template: str
-    required_variables: list[str]
-    is_builtin: bool
-    created_by_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
-@router.post("", response_model=ToolTypeResponse, status_code=status.HTTP_201_CREATED)
-async def create_tool_type(
-    data: ToolTypeCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> ToolType:
-    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(status_code=status.HTTP_409_CONFLICT, detail="tool type with this name already exists")
-    
-    tool_type = ToolType(
-        name=data.name,
-        display_name=data.display_name,
-        description=data.description,
-        compose_template=data.compose_template,
-        required_variables=data.required_variables,
-        is_builtin=False,
-        created_by_id=user.id,
-    )
-    session.add(tool_type)
-    await session.commit()
-    await session.refresh(tool_type)
-    return tool_type
-
-
-@router.get("", response_model=list[ToolTypeResponse])
-async def list_tool_types(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list[ToolType]:
-    await _get_user(session, user_id)
-    result = await session.execute(select(ToolType).order_by(ToolType.name))
-    return list(result.scalars().all())
-
-
-@router.get("/{tool_type_id}", response_model=ToolTypeResponse)
-async def get_tool_type(
-    tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> ToolType:
-    await _get_user(session, user_id)
-    tool_type = await session.get(ToolType, tool_type_id)
-    if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    return tool_type
-
-
-@router.put("/{tool_type_id}", response_model=ToolTypeResponse)
-async def update_tool_type(
-    tool_type_id: uuid.UUID,
-    data: ToolTypeUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> ToolType:
-    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(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    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 required variables if both are being updated
-    if "required_variables" in update_data and "compose_template" in update_data:
-        template = update_data["compose_template"]
-        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:
-        # Only updating variables, check against existing template
-        template = tool_type.compose_template
-        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"
-                )
-    
-    for field, value in update_data.items():
-        setattr(tool_type, field, value)
-    
-    await session.commit()
-    await session.refresh(tool_type)
-    return tool_type
-
-
-@router.delete("/{tool_type_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_tool_type(
-    tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    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(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    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/user/__init__.py

@@ -0,0 +1,7 @@
+"""User API routers module."""
+
+from src.api.user.auth import router as auth_router
+from src.api.user.ssh_keys import router as ssh_keys_router
+from src.api.user.users import router as users_router
+
+__all__ = ["auth_router", "ssh_keys_router", "users_router"]

apps/api/src/api/user/auth.py

@@ -25,8 +25,21 @@ async def get_db_session() -> AsyncGenerator[AsyncSession, None]:
         yield session
 
 
-@router.get("/login")
+@router.get(
+    "/login",
+    summary="Initiate OAuth login",
+    description="Redirects to the configured OAuth provider (Authentik) to start the authentication flow.",
+    response_class=RedirectResponse,
+)
 async def login(next: str = "/") -> RedirectResponse:
+    """Initiate OAuth2 login flow.
+
+    Args:
+        next: URL to redirect to after successful authentication.
+
+    Returns:
+        RedirectResponse to the OAuth provider's authorization endpoint.
+    """
     settings = Settings()
     redirect_uri = f"{settings.api_base_url}/auth/callback"
     state = token_urlsafe(24)
@@ -35,7 +48,7 @@ async def login(next: str = "/") -> RedirectResponse:
         redirect_uri=redirect_uri,
         state=state,
     )
-    logger.info("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
+    logger.debug("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")
@@ -46,12 +59,11 @@ async def login(next: str = "/") -> RedirectResponse:
 async def callback(
     code: str,
     state: str,
-    response: Response,
     auth_state: str | None = Cookie(default=None),
     auth_next: str | None = Cookie(default="/"),
     session: AsyncSession = Depends(get_db_session),
 ) -> RedirectResponse:
-    logger.info("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
+    logger.debug("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)
@@ -59,7 +71,7 @@ async def callback(
 
     settings = Settings()
     redirect_uri = f"{settings.api_base_url}/auth/callback"
-    logger.info("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
+    logger.debug("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
     
     async with httpx.AsyncClient() as client:
         try:
@@ -80,7 +92,7 @@ async def callback(
                 access_token=token_payload["access_token"],
                 client=client,
             )
-            logger.info("User info fetched successfully")
+            logger.debug("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")
@@ -88,19 +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.info("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
+    logger.debug("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.info("Creating new user: authentik_id=%s", authentik_id)
+            logger.debug("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.info("Existing user found: id=%s, updating info", user.id)
+            logger.debug("Existing user found: id=%s, updating info", user.id)
             user.email = email
             user.name = name
             await session.commit()
@@ -116,7 +128,13 @@ async def callback(
     cookie_secure = bool(cookie_options["secure"])
     cookie_domain = str(cookie_options["domain"]) if cookie_options.get("domain") else None
     
-    response.set_cookie(
+    logger.info("Auth callback complete for user id=%s, redirecting to %s", user.id, auth_next)
+    
+    # Redirect to frontend with the original next path
+    redirect_url = f"{settings.web_base_url}{auth_next}"
+    redirect_response = RedirectResponse(url=redirect_url)
+    
+    redirect_response.set_cookie(
         "session", 
         session_cookie, 
         httponly=True, 
@@ -124,14 +142,10 @@ async def callback(
         secure=cookie_secure,
         domain=cookie_domain,
     )
-    response.delete_cookie("auth_state", samesite="lax", domain=cookie_domain)
-    response.delete_cookie("auth_next", samesite="lax", domain=cookie_domain)
+    redirect_response.delete_cookie("auth_state", samesite="lax", domain=cookie_domain)
+    redirect_response.delete_cookie("auth_next", samesite="lax", domain=cookie_domain)
     
-    logger.info("Auth callback complete for user id=%s, redirecting to %s", user.id, auth_next)
-    
-    # Redirect to frontend with the original next path
-    redirect_url = f"{settings.web_base_url}{auth_next}"
-    return RedirectResponse(url=redirect_url)
+    return redirect_response
 
 
 @router.post("/logout")
@@ -151,20 +165,30 @@ 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))
+    
     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", 
+                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)
     except ValueError as exc:
+        logger.warning("Auth /me: invalid session: %s", exc)
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc))
 
     user = await session.get(User, user_id)
     if user is None:
+        logger.warning("Auth /me: user not found for id=%s", user_id)
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
 
+    logger.info("Auth /me: success for user=%s", user.email)
     return {
         "user": {
             "id": str(user.id),

apps/api/src/api/user/ssh_keys.py

@@ -0,0 +1,236 @@
+import base64
+import uuid
+
+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 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.config import Settings
+from src.models import SSHKey
+from src.schemas.project import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
+
+router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
+
+
+def _get_fernet() -> Fernet:
+    """Generate a valid Fernet key from the session secret."""
+    import base64
+    import hashlib
+
+    settings = Settings()
+    # Derive a 32-byte key from the session secret using SHA256
+    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
+    # Base64 encode it for Fernet (must be 32 url-safe base64-encoded bytes)
+    key = base64.urlsafe_b64encode(key_bytes)
+    return Fernet(key)
+
+
+def generate_ssh_key_pair() -> tuple[str, str]:
+    """Generate a new Ed25519 SSH key pair.
+
+    Returns:
+        Tuple of (private_key, public_key) as strings.
+    """
+    private_key = Ed25519PrivateKey.generate()
+    public_key = private_key.public_key()
+
+    private_bytes = private_key.private_bytes(
+        encoding=serialization.Encoding.PEM,
+        format=serialization.PrivateFormat.OpenSSH,
+        encryption_algorithm=serialization.NoEncryption(),
+    )
+
+    public_bytes = public_key.public_bytes(
+        encoding=serialization.Encoding.OpenSSH,
+        format=serialization.PublicFormat.OpenSSH,
+    )
+
+    return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
+
+
+@router.post(
+    "",
+    response_model=SSHKeyResponse,
+    status_code=status.HTTP_201_CREATED,
+    summary="Create SSH key",
+    description="Generate a new Ed25519 SSH key pair for the authenticated user.",
+)
+async def create_ssh_key(
+    data: SSHKeyCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> SSHKey:
+    """Create a new SSH key pair.
+
+    Args:
+        data: SSH key creation data including the key name.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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()
+    encrypted_private = fernet.encrypt(private_key.encode()).decode()
+
+    ssh_key = SSHKey(
+        name=data.name,
+        public_key=public_key,
+        private_key_encrypted=encrypted_private,
+        user_id=user.id,
+    )
+    session.add(ssh_key)
+    await session.commit()
+    await session.refresh(ssh_key)
+    return ssh_key
+
+
+@router.get(
+    "",
+    response_model=list[SSHKeyResponse],
+    summary="List SSH keys",
+    description="List all SSH keys for the authenticated user.",
+)
+async def list_ssh_keys(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[SSHKey]:
+    """List all SSH keys for the authenticated user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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())
+
+
+@router.delete(
+    "/{key_id}",
+    status_code=status.HTTP_204_NO_CONTENT,
+    summary="Delete SSH key",
+    description="Delete an SSH key by ID.",
+)
+async def delete_ssh_key(
+    key_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete an SSH key.
+
+    Args:
+        key_id: UUID of the SSH key to delete.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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/user/users.py

@@ -2,11 +2,11 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import get_current_user_id, get_db_session
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
+from src.schemas.user import UserProfileResponse, UserProfileUpdate
 
 router = APIRouter(prefix="/users", tags=["users"])
 
@@ -16,51 +16,63 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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
-
-
-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", response_model=UserProfileResponse)
+@router.get(
+    "/me",
+    response_model=UserProfileResponse,
+    summary="Get current user profile",
+    description="Retrieve the profile of the currently authenticated user.",
+)
 async def get_profile(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Get the current user's profile.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The user's profile information.
+    """
     return await _get_user(session, user_id)
 
 
-@router.put("/me", response_model=UserProfileResponse)
+@router.put(
+    "/me",
+    response_model=UserProfileResponse,
+    summary="Update user profile",
+    description="Update the current user's profile information.",
+)
 async def update_profile(
     data: UserProfileUpdate,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Update the current user's profile.
+
+    Args:
+        data: Profile update data with optional name and email.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The updated user profile.
+    """
     user = await _get_user(session, user_id)
 
     if data.name is not None:
         if len(data.name.strip()) == 0:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty")
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty"
+            )
         user.name = data.name.strip()
 
     if data.email is not None:
         if "@" not in data.email:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email")
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email"
+            )
         user.email = data.email.strip()
 
     await session.commit()
@@ -68,12 +80,27 @@ async def update_profile(
     return user
 
 
-@router.post("/me/avatar", response_model=UserProfileResponse)
+@router.post(
+    "/me/avatar",
+    response_model=UserProfileResponse,
+    summary="Upload avatar",
+    description="Upload a profile avatar image (PNG or JPG, max 2MB).",
+)
 async def upload_avatar(
     file: UploadFile,
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
+    """Upload a profile avatar image.
+
+    Args:
+        file: The image file to upload (PNG or JPG, max 2MB).
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    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:

apps/api/src/api/user_config.py

@@ -1,74 +0,0 @@
-import uuid
-
-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_current_user_id, get_db_session
-from src.models.user import User
-from src.models.user_config import UserConfig
-
-router = APIRouter(prefix="/users/me", tags=["user-config"])
-
-
-async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
-    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_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
-    result = await session.execute(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={})
-        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
-
-
-class UserConfigUpdate(BaseModel):
-    default_editor: str | None = None
-    theme: str | None = None
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-
-
-@router.get("/config", response_model=UserConfigResponse)
-async def get_user_config(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> UserConfigResponse:
-    _user = await _get_user(session, user_id)
-    config = await _get_or_create_config(session, user_id)
-    return UserConfigResponse.model_validate(config.config)
-
-
-@router.patch("/config", response_model=UserConfigResponse)
-async def update_user_config(
-    data: UserConfigUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> UserConfigResponse:
-    _user = await _get_user(session, user_id)
-    config = await _get_or_create_config(session, user_id)
-
-    # Merge updates
-    update_data = data.model_dump(exclude_unset=True, exclude_none=True)
-    config.config.update(update_data)
-
-    await session.commit()
-    await session.refresh(config)
-    return UserConfigResponse.model_validate(config.config)

apps/api/src/api/workspace/__init__.py

@@ -0,0 +1,17 @@
+"""Workspace API routers module."""
+
+from src.api.workspace.workspace_files import router as workspace_files_router
+from src.api.workspace.workspace_git import router as workspace_git_router
+from src.api.workspace.workspace_instances import router as workspace_instances_router
+from src.api.workspace.workspaces import (
+    all_workspaces_router,
+    router as workspaces_router,
+)
+
+__all__ = [
+    "all_workspaces_router",
+    "workspace_files_router",
+    "workspace_git_router",
+    "workspace_instances_router",
+    "workspaces_router",
+]

apps/api/src/api/workspace/workspace_files.py

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

apps/api/src/api/workspace/workspace_git.py

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

apps/api/src/api/workspace/workspace_instances.py

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

apps/api/src/api/workspace/workspaces.py

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

apps/api/src/auth/dependencies.py

@@ -7,6 +7,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.session import decode_session_cookie
 from src.config import Settings
 from src.database import SessionLocal
+from src.models.project import Project
 from src.models.user import User
 
 
@@ -47,3 +48,39 @@ async def get_current_user(
     if user is None:
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="user not found")
     return user
+
+
+async def _get_user(session: AsyncSession, user_id: uuid.UUID) -> User:
+    """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,
+    session: AsyncSession,
+) -> "Project":
+    """Fetch a project and verify ownership.
+
+    Args:
+        project_id: UUID of the project.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        The project if found and owned by the user.
+
+    Raises:
+        HTTPException: 404 if project not found, 403 if user is not the owner.
+    """
+    from src.models.project import Project
+
+    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:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not project owner")
+    return project

apps/api/src/auth/session.py

@@ -2,7 +2,7 @@ import hmac
 import hashlib
 import json
 import base64
-from datetime import UTC, datetime, timedelta
+from datetime import datetime, timedelta, timezone
 from typing import Any
 
 from src.config import Settings
@@ -23,7 +23,7 @@ def create_session_cookie(*, settings: Settings, user_id: str) -> str:
     """Create a signed session cookie value."""
     payload = {
         "user_id": user_id,
-        "exp": int((datetime.now(UTC) + timedelta(hours=settings.session_ttl_hours)).timestamp()),
+        "exp": int((datetime.now(timezone.utc) + timedelta(hours=settings.session_ttl_hours)).timestamp()),
     }
     
     header = _base64url_encode(json.dumps({"alg": "HS256", "typ": "session"}).encode())
@@ -65,7 +65,7 @@ def decode_session_cookie(*, settings: Settings, cookie_value: str) -> dict[str,
     payload = json.loads(payload_bytes)
     
     # Check expiry
-    if payload.get("exp", 0) < int(datetime.now(UTC).timestamp()):
+    if payload.get("exp", 0) < int(datetime.now(timezone.utc).timestamp()):
         raise ValueError("session expired")
     
     return payload

apps/api/src/config.py

@@ -50,6 +50,11 @@ class Settings(BaseSettings):
     # Repository storage
     repo_base_path: str = "/data/repos"
     
+    # Tool instance storage
+    instance_base_path: str = "/data/instances"
+
+
+
     model_config = SettingsConfigDict(env_file=".env", extra="ignore", populate_by_name=True)
 
     @property

apps/api/src/logging_config.py

@@ -1,15 +1,52 @@
+"""Structured JSON logging configuration."""
+
+import json
 import logging
 import sys
 import time
 import traceback
-from typing import Callable
+from collections.abc import Callable
 
 from fastapi import Request, Response
 from starlette.middleware.base import BaseHTTPMiddleware
 
+from src.services.shared.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."""
 
@@ -17,7 +54,6 @@ 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,
@@ -29,7 +65,6 @@ 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,
@@ -69,15 +104,13 @@ class ExceptionLoggingMiddleware(BaseHTTPMiddleware):
 
 
 def configure_logging(level: int = logging.INFO) -> None:
-    """Configure structured logging for the application."""
-    formatter = logging.Formatter(
-        fmt="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-    )
+    """Configure structured JSON logging for the application."""
+    formatter = JSONFormatter()
 
     # 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

@@ -1,29 +1,48 @@
 import logging
 import os
 
-from fastapi import FastAPI
+from fastapi import FastAPI, Request
+from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
-from sqlalchemy import select, text
 
-from src.api.auth import router as auth_router
-from src.api.dashboard import router as dashboard_router
-from src.api.git_repositories import router as git_repositories_router
-from src.api.projects import router as projects_router
-from src.api.ssh_keys import router as ssh_keys_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.user_config import router as user_config_router
-from src.api.users import router as users_router
+from src.api.config import config_profiles_router, user_config_router
+from src.api.project import git_repositories_router, projects_router
+from src.api.system import (
+    dashboard_router,
+    events_router,
+    health_router,
+    instance_proxy_router,
+    notifications_router,
+    terminal_router,
+)
+from src.api.tool import (
+    sessions_router,
+    tool_definitions_router,
+    tool_instances_router,
+    tool_types_router,
+)
+from src.api.user import auth_router, ssh_keys_router, users_router
+from src.api.workspace import (
+    all_workspaces_router,
+    workspace_files_router,
+    workspace_git_router,
+    workspace_instances_router,
+    workspaces_router,
+)
 from src.config import Settings
-from src.database import SessionLocal, init_database
+from src.models import Notification  # noqa: F401 – Alembic model discovery
+from src.models import TerminalSessionModel  # noqa: F401 – Alembic model discovery
+from src.database import init_database
 from src.logging_config import (
     ExceptionLoggingMiddleware,
     RequestLoggingMiddleware,
     configure_logging,
 )
-from src.models.tool_type import ToolType
+from src.seeds.builtin_tool_types import seed_builtin_tool_types
+from src.services.instance import InstanceEventBus, HealthMonitor
+from src.services.shared import CorrelationIdMiddleware
 
 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -34,102 +53,73 @@ settings = Settings()
 app = FastAPI(title="Headquarter API")
 
 # Configure CORS - must be before other middleware
+# Build allowed origins list including web and api domains
+cors_origins = [settings.web_base_url]
+if settings.api_base_url != settings.web_base_url:
+    cors_origins.append(settings.api_base_url)
+logger.info("CORS configured with origins: %s", cors_origins)
+
 app.add_middleware(
     CORSMiddleware,
-    allow_origins=[settings.web_base_url],
+    allow_origins=cors_origins,
     allow_credentials=True,
     allow_methods=["*"],
     allow_headers=["*"],
 )
 
+app.add_middleware(CorrelationIdMiddleware)
 app.add_middleware(RequestLoggingMiddleware)
 app.add_middleware(ExceptionLoggingMiddleware)
 
 
-async def _table_exists(session, table_name: str) -> bool:
-    """Check if a table exists in the database."""
-    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
+def _sanitize_validation_errors(errors):
+    """Convert validation errors to JSON-safe format."""
+    sanitized = []
+    for error in errors:
+        safe_error = {
+            "type": error.get("type"),
+            "loc": error.get("loc"),
+            "msg": error.get("msg"),
+            "input": str(error.get("input"))
+            if error.get("input") is not None
+            else None,
+        }
+        # Convert ctx to safe format
+        ctx = error.get("ctx")
+        if ctx:
+            safe_ctx = {}
+            for key, value in ctx.items():
+                if isinstance(value, Exception):
+                    safe_ctx[key] = str(value)
+                elif isinstance(value, (str, int, float, bool, type(None))):
+                    safe_ctx[key] = value
+                else:
+                    safe_ctx[key] = str(value)
+            safe_error["ctx"] = safe_ctx
+        sanitized.append(safe_error)
+    return sanitized
 
 
-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"):
+@app.exception_handler(RequestValidationError)
+async def validation_exception_handler(request: Request, exc: RequestValidationError):
+    """Log validation errors and return detailed response."""
+    errors = exc.errors()
     logger.warning(
-                "tool_types table does not exist. Skipping seeding. "
-                "Migrations may not have run yet."
+        "Validation error for %s %s: %s",
+        request.method,
+        request.url.path,
+        errors,
     )
-            return
-
-        builtin_types = [
-            {
-                "name": "code-server",
-                "display_name": "VS Code Server",
-                "description": "VS Code running in the browser via code-server",
-                "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""",
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-            {
-                "name": "jupyter-notebook",
-                "display_name": "Jupyter Notebook",
-                "description": "Jupyter Lab for interactive development",
-                "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"],
-            },
-        ]
-
-        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"],
-                    compose_template=tool_data["compose_template"],
-                    required_variables=tool_data["required_variables"],
-                    is_builtin=True,
+    safe_errors = _sanitize_validation_errors(errors)
+    return JSONResponse(
+        status_code=422,
+        content={"detail": safe_errors},
     )
-                session.add(tool_type)
 
-        await session.commit()
-        logger.info("Built-in tool types seeded successfully.")
+
+# Global services
+_event_bus = InstanceEventBus()
+_health_monitor = HealthMonitor(_event_bus)
 
 
 @app.on_event("startup")
@@ -141,23 +131,29 @@ async def on_startup():
     if not db_ready:
         logger.error("Database initialization failed. Shutting down.")
         import sys
+
         sys.exit(1)
 
-    # Seed built-in data
+    # Start background health monitor
+    _health_monitor.start()
+    logger.info("Health monitor started")
+
+    # Seed built-in tool types
     await seed_builtin_tool_types()
+    logger.info("Built-in tool types seeded")
+
     logger.info("Startup complete.")
 
-@app.get("/health")
-async def health_check():
-    try:
-        from sqlalchemy import text
-        async with SessionLocal() as session:
-            await session.execute(text("SELECT 1"))
-        return {"status": "healthy", "database": "connected"}
-    except Exception as exc:
-        logger.error("Health check failed: %s", exc)
-        return {"status": "unhealthy", "database": "disconnected", "error": str(exc)}
 
+@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)
 app.include_router(projects_router)
@@ -166,6 +162,17 @@ 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_profiles_router)
 app.include_router(tool_instances_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.include_router(all_workspaces_router)
+app.include_router(workspaces_router)
+app.include_router(workspace_files_router)
+app.include_router(workspace_git_router)
+app.include_router(workspace_instances_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")

apps/api/src/models/__init__.py

@@ -1,10 +1,34 @@
 from src.models.base import Base
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.models.user_config import UserConfig
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.project.git_repository import GitRepository
+from src.models.project.project import Project
+from src.models.project.workspace import Workspace
+from src.models.system.health_check import HealthCheck
+from src.models.system.instance_event import InstanceEvent
+from src.models.system.notification import Notification
+from src.models.system.terminal_session import TerminalSessionModel
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool.tool_instance import ToolInstance
+from src.models.tool.tool_type import ToolType
+from src.models.user.ssh_key import SSHKey
+from src.models.user.user import User
+from src.models.user.user_config import UserConfig
 
-__all__ = ["Base", "GitRepository", "Project", "SSHKey", "ToolInstance", "ToolType", "User", "UserConfig"]
+__all__ = [
+    "Base",
+    "ConfigProfile",
+    "ConfigProfileInclude",
+    "GitRepository",
+    "HealthCheck",
+    "InstanceEvent",
+    "Notification",
+    "Project",
+    "SSHKey",
+    "TerminalSessionModel",
+    "ToolDefinitionManifest",
+    "ToolInstance",
+    "ToolType",
+    "User",
+    "UserConfig",
+    "Workspace",
+]

apps/api/src/models/config/__init__.py

@@ -0,0 +1,5 @@
+"""Config models module."""
+
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
+
+__all__ = ["ConfigProfile", "ConfigProfileInclude"]

apps/api/src/models/config/config_profile.py

@@ -0,0 +1,88 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import (
+    Boolean,
+    ForeignKey,
+    JSON,
+    Integer,
+    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.project import Project
+    from src.models import ToolType
+    from src.models.user import User
+
+
+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(
+        JSON, default=dict, nullable=False
+    )  # {"VAR_NAME": "value", ...}
+    runtime_hints: Mapped[dict] = mapped_column(
+        JSON, default=dict, nullable=False
+    )  # {"start_command": "...", "working_dir": "...", ...}
+    mounts: Mapped[list] = mapped_column(
+        JSON, default=list, nullable=False
+    )  # [{"target": "/path", "mode": "rw", "files": {"rel/path": "content"}}, ...]
+    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(
+        "ConfigProfileInclude",
+        foreign_keys="ConfigProfileInclude.profile_id",
+        order_by="ConfigProfileInclude.order_index",
+        cascade="all, delete-orphan",
+    )
+
+
+class ConfigProfileInclude(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "config_profile_includes"
+
+    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/project/__init__.py

@@ -0,0 +1,7 @@
+"""Project models module."""
+
+from src.models.project.git_repository import GitRepository
+from src.models.project.project import Project
+from src.models.project.workspace import Workspace
+
+__all__ = ["GitRepository", "Project", "Workspace"]

apps/api/src/models/project/git_repository.py

@@ -10,6 +10,7 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
+    from src.models import SSHKey
     from src.models.user import User
 
 
@@ -18,11 +19,15 @@ class GitRepository(UUIDPrimaryKeyMixin, TimestampMixin, Base):
 
     name: Mapped[str] = mapped_column(String(255))
     path: Mapped[str] = mapped_column(String(1024))
-    project_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=False)
+    project_id: Mapped[uuid.UUID | None] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=True)
     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()