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`.

.gitignore

@@ -49,3 +49,8 @@ apps/web/dist/
 .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"
+    }
+  }
+}

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.
 

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

@@ -50,8 +50,8 @@ ENV PATH=/root/.local/bin:$PATH
 # Copy application code
 COPY --chown=appuser:appgroup . .
 
-# Create directories for repo and instance storage
-RUN mkdir -p /data/repos /data/instances && chown -R appuser:appgroup /data
+# 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

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/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/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/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/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/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

@@ -1,25 +1,37 @@
 """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 pydantic import BaseModel, Field, field_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
-from src.api.shared_validators import validate_env_vars as _validate_env_vars
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models import ConfigProfile, ConfigProfileInclude
 from src.models.project import Project
-from src.models.tool_type import ToolType
-from src.services.config_profile_resolver import (
+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__)
 
@@ -29,16 +41,6 @@ MAX_PROFILE_SIZE_MB = 10
 MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
 
 
-def _validate_uuid(v: str | None) -> str | None:
-    if v is None:
-        return v
-    try:
-        uuid.UUID(v)
-    except ValueError:
-        raise ValueError(f"Invalid UUID: {v}")
-    return v
-
-
 def _calculate_profile_size(data: dict) -> int:
     """Calculate approximate serialized size of profile data."""
     total = 0
@@ -56,183 +58,9 @@ def _calculate_profile_size(data: dict) -> int:
     return total
 
 
-class GitMountItem(BaseModel):
-    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
-    source_path: str = Field(default=".", description="Path within repository (supports glob patterns)")
-    target_path: str = Field(description="Absolute path inside container")
-    branch: str | None = Field(default=None, description="Optional branch or tag name")
-
-    @field_validator("remote_url")
-    @classmethod
-    def validate_remote_url(cls, v: str) -> str:
-        if not v.startswith(("http://", "https://", "git@", "ssh://")):
-            raise ValueError("remote_url must be a valid git URL (https://, git@, or ssh://)")
-        return v
-
-    @field_validator("source_path")
-    @classmethod
-    def validate_source_path(cls, v: str) -> str:
-        if v.startswith("/"):
-            raise ValueError("source_path must be relative (no leading /)")
-        if ".." in v:
-            raise ValueError("source_path cannot contain path traversal (..)")
-        return v
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str) -> str:
-        if ".." in v:
-            raise ValueError("target_path cannot contain path traversal (..)")
-        return v
-
-
-class MountItem(BaseModel):
-    target: str = Field(description="Absolute mount target path")
-    mode: str = Field(default="rw", description="Mount mode: ro or rw")
-    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
-
-    @field_validator("target")
-    @classmethod
-    def validate_target(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("Mount target must be absolute (start with /)")
-        return v
-
-    @field_validator("mode")
-    @classmethod
-    def validate_mode(cls, v: str) -> str:
-        if v not in ("ro", "rw"):
-            raise ValueError("Mount mode must be 'ro' or 'rw'")
-        return v
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"Mount file paths must be relative (got: {path}). "
-                    f"The mount target defines the absolute container path."
-                )
-        return v
-
-
-class ConfigProfileCreate(BaseModel):
-    name: str = Field(description="Profile name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict = Field(default_factory=dict, description="Environment variables")
-    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
-    mounts: list[MountItem] = Field(default_factory=list, description="Mount definitions")
-    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
-    git_mounts: list[GitMountItem] = Field(default_factory=list, description="Git repository mounts")
-    is_default: bool = Field(default=False, description="Whether this is the default profile for its scope")
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"File paths must be relative (got: {path}). "
-                    f"Use Mounts for absolute container paths."
-                )
-        return v
-
-    @field_validator("env_vars")
-    @classmethod
-    def validate_env_vars(cls, v: dict) -> dict:
-        result = _validate_env_vars(v)
-        if result is None:
-            raise ValueError("env_vars must be a JSON object")
-        return result
-
-    @field_validator("runtime_hints")
-    @classmethod
-    def validate_runtime_hints(cls, v: dict) -> dict:
-        if not isinstance(v, dict):
-            raise ValueError("runtime_hints must be a JSON object")
-        return v
-
-    @field_validator("mounts")
-    @classmethod
-    def validate_mounts(cls, v: list) -> list:
-        if not isinstance(v, list):
-            raise ValueError("mounts must be a JSON array")
-        return v
-
-
-class ConfigProfileUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Profile name")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict | None = Field(default=None, description="Environment variables")
-    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
-    mounts: list[MountItem] | None = Field(default=None, description="Mount definitions")
-    files: dict | None = Field(default=None, description="Files as {relative_path: content}")
-    git_mounts: list[GitMountItem] | None = Field(default=None, description="Git repository mounts")
-    is_default: bool | None = Field(default=None, description="Whether this is the default profile")
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        for path in v.keys():
-            if ".." in path or path.startswith("/") or not path:
-                raise ValueError(f"Invalid file path: {path}")
-        return v
-
-
-class ConfigProfileIncludeUpdate(BaseModel):
-    includes: list[str] = Field(description="Ordered list of included profile IDs")
-
-    @field_validator("includes")
-    @classmethod
-    def validate_includes(cls, v: list) -> list:
-        for item in v:
-            try:
-                uuid.UUID(item)
-            except ValueError:
-                raise ValueError(f"Invalid UUID in includes: {item}")
-        return v
-
-
-class ConfigProfileResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    project_id: str | None
-    tool_type_id: str | None
-    env_vars: dict
-    runtime_hints: dict
-    mounts: list
-    files: dict
-    git_mounts: list
-    is_default: bool
-    includes: list[dict]
-    created_at: str
-    updated_at: str
-
-
-async def _get_profile_with_includes(session: AsyncSession, profile_id: uuid.UUID) -> ConfigProfile | None:
+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)
@@ -252,22 +80,26 @@ async def _check_access(
     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")
+            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")
+            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[dict],
+    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.
     """
@@ -278,7 +110,7 @@ async def _validate_git_mounts(
                 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,
@@ -286,7 +118,9 @@ async def _validate_git_mounts(
             )
 
 
-def _profile_to_response(profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None) -> dict:
+def _profile_to_response(
+    profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None
+) -> dict:
     return {
         "id": str(profile.id),
         "user_id": str(profile.user_id),
@@ -316,13 +150,19 @@ def _profile_to_response(profile: ConfigProfile, includes: list[ConfigProfileInc
 @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"),
+    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))
+    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
@@ -334,7 +174,8 @@ async def list_config_profiles(
         conditions: list = []
         # Portable profiles (no project, no tool)
         conditions.append(
-            (ConfigProfile.project_id.is_(None)) & (ConfigProfile.tool_type_id.is_(None))
+            (ConfigProfile.project_id.is_(None))
+            & (ConfigProfile.tool_type_id.is_(None))
         )
         if project_uuid:
             # Profiles matching this project (with or without tool)
@@ -345,7 +186,8 @@ async def list_config_profiles(
         if project_uuid and tool_uuid:
             # Exact match
             conditions.append(
-                (ConfigProfile.project_id == project_uuid) & (ConfigProfile.tool_type_id == tool_uuid)
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
             )
 
         query = query.where(or_(*conditions))
@@ -355,7 +197,9 @@ async def list_config_profiles(
     return [_profile_to_response(p) for p in profiles]
 
 
-@router.post("", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED)
+@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),
@@ -366,10 +210,12 @@ async def create_config_profile(
 
     # Check for duplicate name
     existing = await session.execute(
-        select(ConfigProfile).where(
+        select(ConfigProfile)
+        .where(
             ConfigProfile.user_id == user_uuid,
             ConfigProfile.name == data.name,
-        ).options(selectinload(ConfigProfile.includes))
+        )
+        .options(selectinload(ConfigProfile.includes))
     )
     if existing.scalar_one_or_none() is not None:
         raise HTTPException(
@@ -381,10 +227,12 @@ async def create_config_profile(
     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]
+        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
@@ -432,9 +280,13 @@ async def get_config_profile(
     """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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
     return _profile_to_response(profile)
 
 
@@ -448,9 +300,13 @@ async def update_config_profile(
     """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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
 
     update_data = data.model_dump(exclude_unset=True)
 
@@ -481,14 +337,16 @@ async def update_config_profile(
         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 
+            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)
+        await _validate_git_mounts(
+            session, profile.user_id, git_mounts_data, project_uuid
+        )
 
     # Check size
     current_data = _profile_to_response(profile)
@@ -533,9 +391,13 @@ async def delete_config_profile(
     """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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
 
     await session.delete(profile)
     await session.commit()
@@ -554,9 +416,13 @@ async def update_profile_includes(
     """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")
+        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")
+        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]
@@ -596,7 +462,9 @@ async def update_profile_includes(
 
     # Remove existing includes
     result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
     )
     for existing in result.scalars().all():
         await session.delete(existing)
@@ -621,7 +489,9 @@ async def update_profile_includes(
     profile = result.scalar_one()
 
     inc_result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
     )
     direct_includes = inc_result.scalars().all()
 
@@ -638,9 +508,13 @@ async def preview_config_profile(
     """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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
 
     try:
         resolved = await resolve_profile(session, profile.id)
@@ -721,3 +595,248 @@ async def resolve_default_profile(
     # 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

@@ -2,19 +2,21 @@ import logging
 import uuid
 
 from fastapi import APIRouter, Depends
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.user_config import UserConfig
+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:
+async def _get_or_create_config(
+    session: AsyncSession, user_id: uuid.UUID
+) -> UserConfig:
     """Get or create user config record.
 
     Args:
@@ -24,7 +26,9 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     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))
+    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={})
@@ -34,24 +38,6 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     return config
 
 
-class UserConfigResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    default_editor: str | None = None
-    theme: str = "system"
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-
-
-class UserConfigUpdate(BaseModel):
-    default_editor: str | None = None
-    theme: str | None = None
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-
-
 @router.get(
     "/config",
     response_model=UserConfigResponse,

apps/api/src/api/config_folders.py

@@ -1,337 +0,0 @@
-"""Config folder API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, Field, field_validator
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.api.shared_validators import validate_files as _validate_files, validate_mount_path as _validate_mount_path
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_folder import ConfigFolder
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-folders", tags=["config-folders"])
-
-
-class ConfigFolderCreate(BaseModel):
-    name: str = Field(description="Folder name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-    mount_path: str = Field(description="Default mount path in container")
-    files: dict = Field(default_factory=dict, description="Files as {path: content}")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str) -> str:
-        return _validate_mount_path(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        return _validate_files(v)
-
-
-class ConfigFolderUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Folder name")
-    description: str | None = Field(default=None, description="Optional description")
-    mount_path: str | None = Field(default=None, description="Default mount path")
-    files: dict | None = Field(default=None, description="Files as {path: content}")
-    is_active: bool | None = Field(default=None, description="Active/inactive toggle")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str | None) -> str | None:
-        return _validate_mount_path(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict | None) -> dict | None:
-        return _validate_files(v)
-
-
-class ProjectOverrideCreate(BaseModel):
-    mount_path: str | None = Field(default=None, description="Override mount path")
-    files: dict = Field(default_factory=dict, description="Override files")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str | None) -> str | None:
-        return _validate_mount_path(v)
-
-
-class ConfigFolderResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    mount_path: str
-    files: dict
-    project_overrides: dict | None
-    is_active: bool
-    created_at: str
-    updated_at: str
-
-
-@router.get("", summary="List config folders", description="Get all config folders for the current user.")
-async def list_config_folders(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List config folders for the current user."""
-    query = select(ConfigFolder).where(ConfigFolder.user_id == user_id)
-    result = await session.execute(query)
-    folders = result.scalars().all()
-    
-    return {
-        "folders": [
-            {
-                "id": str(f.id),
-                "user_id": str(f.user_id),
-                "name": f.name,
-                "description": f.description,
-                "mount_path": f.mount_path,
-                "files": f.files,
-                "project_overrides": f.project_overrides,
-                "is_active": f.is_active,
-                "created_at": f.created_at.isoformat() if f.created_at else None,
-                "updated_at": f.updated_at.isoformat() if f.updated_at else None,
-            }
-            for f in folders
-        ]
-    }
-
-
-@router.post("", summary="Create config folder", description="Create a new config folder.", status_code=status.HTTP_201_CREATED)
-async def create_config_folder(
-    data: ConfigFolderCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a config folder."""
-    # Check for duplicate name
-    existing = await session.scalar(
-        select(ConfigFolder).where(
-            ConfigFolder.user_id == user_id,
-            ConfigFolder.name == data.name,
-        )
-    )
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"config folder with name '{data.name}' already exists"
-        )
-    
-    folder = ConfigFolder(
-        user_id=user_id,
-        name=data.name,
-        description=data.description,
-        mount_path=data.mount_path,
-        files=data.files,
-    )
-    session.add(folder)
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.put("/{folder_id}", summary="Update config folder", description="Update an existing config folder.")
-async def update_config_folder(
-    folder_id: uuid.UUID,
-    data: ConfigFolderUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    if data.name is not None:
-        folder.name = data.name
-    if data.description is not None:
-        folder.description = data.description
-    if data.mount_path is not None:
-        folder.mount_path = data.mount_path
-    if data.files is not None:
-        folder.files = data.files
-    if data.is_active is not None:
-        folder.is_active = data.is_active
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.delete("/{folder_id}", summary="Delete config folder", description="Delete a config folder.", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_folder(
-    folder_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    await session.delete(folder)
-    await session.commit()
-
-
-class ProjectOverrideWithId(ProjectOverrideCreate):
-    project_id: uuid.UUID = Field(description="Project ID for the override")
-
-
-@router.get("/{folder_id}", summary="Get config folder by ID", description="Get a single config folder by its ID.")
-async def get_config_folder(
-    folder_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a config folder by ID."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.post("/{folder_id}/overrides", summary="Add project override", description="Add a project override to a config folder.")
-async def add_project_override(
-    folder_id: uuid.UUID,
-    data: ProjectOverrideWithId,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Add a project override to a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Initialize project_overrides if None
-    if folder.project_overrides is None:
-        folder.project_overrides = {}
-    
-    # Add/update override
-    override_data = {}
-    if data.mount_path is not None:
-        override_data["mount_path"] = data.mount_path
-    if data.files is not None:
-        override_data["files"] = data.files
-    
-    # Use a copy to trigger SQLAlchemy change detection on JSONB
-    current_overrides = dict(folder.project_overrides or {})
-    current_overrides[str(data.project_id)] = override_data
-    folder.project_overrides = current_overrides
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides,
-    }
-
-
-@router.put("/{folder_id}/overrides/{project_id}", summary="Update project override", description="Update a project override.")
-async def update_project_override(
-    folder_id: uuid.UUID,
-    project_id: uuid.UUID,
-    data: ProjectOverrideCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a project override."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Initialize project_overrides if None
-    if folder.project_overrides is None:
-        folder.project_overrides = {}
-    
-    # Update override
-    current_overrides = dict(folder.project_overrides or {})
-    override_data = current_overrides.get(str(project_id), {})
-    if data.mount_path is not None:
-        override_data["mount_path"] = data.mount_path
-    if data.files is not None:
-        override_data["files"] = data.files
-    
-    current_overrides[str(project_id)] = override_data
-    folder.project_overrides = current_overrides
-    
-    # Mark the field as modified to ensure SQLAlchemy detects the change
-    from sqlalchemy.orm.attributes import flag_modified
-    flag_modified(folder, "project_overrides")
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides,
-    }
-
-
-@router.delete("/{folder_id}/overrides/{project_id}", summary="Remove project override", description="Remove a project override.")
-async def remove_project_override(
-    folder_id: uuid.UUID,
-    project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Remove a project override."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Remove override if exists
-    current_overrides = dict(folder.project_overrides or {})
-    if str(project_id) in current_overrides:
-        del current_overrides[str(project_id)]
-        folder.project_overrides = current_overrides
-        await session.commit()
-        await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides or {},
-    }

apps/api/src/api/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/git_repositories.py

@@ -3,17 +3,28 @@ 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 pydantic import BaseModel
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
 from src.config import Settings
-from src.models.git_repository import GitRepository
-from src.models.ssh_key import SSHKey
+from src.models import GitRepository
+from src.models import SSHKey
+from src.schemas.project import (
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    URLParseRequest,
+    URLParseResponse,
+    UpdateSSHKeyRequest,
+)
 from src.utils.git_files import (
     commit_file,
     get_file_content,
@@ -33,7 +44,7 @@ from src.utils.git_control import (
 )
 from src.utils.git_history import get_commit_detail, get_commit_history
 from src.utils.git_url_parser import parse_git_url
-from src.services.ssh_keys import _get_fernet
+from src.services.shared.ssh_keys import _get_fernet
 
 router = APIRouter(prefix="/projects", tags=["git-repositories"])
 
@@ -62,19 +73,19 @@ def _build_provider_clone_url(owner: str, repo: str) -> str:
 
 def _prepare_ssh_env(ssh_key: SSHKey | None) -> dict | None:
     """Prepare environment variables for git commands with SSH authentication.
-    
+
     Returns a dict of extra env vars, or None if no SSH key provided.
     The caller is responsible for cleaning up the temporary key file.
     """
     if ssh_key is None:
         return None
-    
+
     import tempfile
-    
+
     # Decrypt private key
     fernet = _get_fernet()
     private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
-    
+
     # Write to temp file with restricted permissions
     fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
     try:
@@ -82,7 +93,7 @@ def _prepare_ssh_env(ssh_key: SSHKey | None) -> dict | None:
     finally:
         os.close(fd)
     os.chmod(key_path, 0o600)
-    
+
     # Return env vars and the key path for cleanup
     env = {
         "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
@@ -90,16 +101,18 @@ def _prepare_ssh_env(ssh_key: SSHKey | None) -> dict | None:
     return env, key_path
 
 
-def _preflight_remote_repository(remote_url: str, ssh_key: SSHKey | None = None) -> None:
+def _preflight_remote_repository(
+    remote_url: str, ssh_key: SSHKey | None = None
+) -> None:
     """Verify a remote repository is reachable before cloning."""
     env = None
     key_path = None
-    
+
     if ssh_key is not None:
         ssh_result = _prepare_ssh_env(ssh_key)
         if ssh_result:
             env, key_path = ssh_result
-    
+
     try:
         result = subprocess.run(
             ["git", "ls-remote", remote_url],
@@ -109,30 +122,40 @@ def _preflight_remote_repository(remote_url: str, ssh_key: SSHKey | None = None)
             env={**os.environ, **env} if env else None,
         )
     except subprocess.TimeoutExpired:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="remote repository check timed out")
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="remote repository check timed out",
+        )
     except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail="git command not found",
+        )
     finally:
         if key_path and os.path.exists(key_path):
             os.unlink(key_path)
 
     if result.returncode != 0:
-        logger.error("Preflight check failed for %s: stderr=%s", remote_url, result.stderr)
+        logger.error(
+            "Preflight check failed for %s: stderr=%s", remote_url, result.stderr
+        )
         raise HTTPException(
             status_code=status.HTTP_400_BAD_REQUEST,
             detail=f"repository not found or inaccessible: {result.stderr}",
         )
 
 
-def _clone_working_repository(remote_url: str, repo_path: str, ssh_key: SSHKey | None = None) -> None:
+def _clone_working_repository(
+    remote_url: str, repo_path: str, ssh_key: SSHKey | None = None
+) -> None:
     env = None
     key_path = None
-    
+
     if ssh_key is not None:
         ssh_result = _prepare_ssh_env(ssh_key)
         if ssh_result:
             env, key_path = ssh_result
-    
+
     try:
         result = subprocess.run(
             ["git", "clone", remote_url, repo_path],
@@ -142,9 +165,14 @@ def _clone_working_repository(remote_url: str, repo_path: str, ssh_key: SSHKey |
             env={**os.environ, **env} if env else None,
         )
     except subprocess.TimeoutExpired:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="clone operation timed out")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail="git command not found",
+        )
     finally:
         if key_path and os.path.exists(key_path):
             os.unlink(key_path)
@@ -165,7 +193,10 @@ def _init_working_repository(repo_path: str) -> None:
             text=True,
         )
     except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail="git command not found",
+        )
 
     if result.returncode == 0:
         return
@@ -193,43 +224,6 @@ def _init_working_repository(repo_path: str) -> None:
         )
 
 
-class GitRepositoryCreate(BaseModel):
-    name: str
-    remote_url: str | None = None
-    force_original_url: bool = False
-    ssh_key_id: str | None = None
-
-
-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 | None
-    owner_id: uuid.UUID
-    is_mirror: bool
-    remote_url: str | None
-    last_push: datetime | None
-    ssh_key_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
 @router.get(
     "/repositories",
     response_model=list[GitRepositoryResponse],
@@ -310,7 +304,10 @@ async def create_external_repository(
         )
     )
     if existing.scalar_one_or_none():
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+        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
@@ -336,13 +333,21 @@ async def create_external_repository(
         try:
             ssh_key_id = uuid.UUID(data.ssh_key_id)
         except ValueError:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
-        
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="invalid ssh_key_id format",
+            )
+
         ssh_key = await session.get(SSHKey, ssh_key_id)
         if ssh_key is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+            )
         if ssh_key.user_id != user_id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user")
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="ssh key does not belong to user",
+            )
 
     if remote_url:
         _preflight_remote_repository(remote_url, ssh_key)
@@ -369,7 +374,10 @@ async def create_external_repository(
             repo.is_mirror = False
         except Exception as exc:
             await session.rollback()
-            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Failed to clone repository: {exc}")
+            raise HTTPException(
+                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+                detail=f"Failed to clone repository: {exc}",
+            )
     else:
         # Initialize empty repo
         os.makedirs(repo_path, exist_ok=True)
@@ -438,7 +446,9 @@ async def delete_repository(
 
     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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found"
+        )
 
     # Remove from disk
     if os.path.exists(repo.path):
@@ -484,7 +494,10 @@ async def create_repository(
         )
     )
     if existing.scalar_one_or_none():
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+        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
@@ -511,13 +524,21 @@ async def create_repository(
         try:
             ssh_key_id = uuid.UUID(data.ssh_key_id)
         except ValueError:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
-        
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="invalid ssh_key_id format",
+            )
+
         ssh_key = await session.get(SSHKey, ssh_key_id)
         if ssh_key is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+            )
         if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="ssh key does not belong to user or project",
+            )
 
     if remote_url:
         _preflight_remote_repository(remote_url, ssh_key)
@@ -547,10 +568,6 @@ async def create_repository(
     return repo
 
 
-class UpdateSSHKeyRequest(BaseModel):
-    ssh_key_id: str | None = None
-
-
 @router.patch(
     "/{project_id}/repositories/{repo_id}/ssh-key",
     response_model=GitRepositoryResponse,
@@ -581,20 +598,30 @@ async def update_repository_ssh_key(
 
     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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found"
+        )
 
     # Validate SSH key if provided
     if data.ssh_key_id:
         try:
             ssh_key_id = uuid.UUID(data.ssh_key_id)
         except ValueError:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail="invalid ssh_key_id format",
+            )
 
         ssh_key = await session.get(SSHKey, ssh_key_id)
         if ssh_key is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+            )
         if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+            raise HTTPException(
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="ssh key does not belong to user or project",
+            )
 
         repo.ssh_key_id = ssh_key_id
     else:
@@ -640,16 +667,24 @@ async def get_repository_history(
 
     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")
+        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")
+        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)
+        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))
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e)
+        )
 
 
 @router.get(
@@ -681,10 +716,14 @@ async def get_repository_commit(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         detail = get_commit_detail(repo.path, commit_hash)
@@ -763,10 +802,14 @@ async def list_repository_files(
 
     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")
+        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")
+        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)
@@ -829,10 +872,14 @@ async def get_repository_file_content(
 
     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")
+        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")
+        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)
@@ -847,7 +894,9 @@ async def get_repository_file_content(
             last_commit=file_content.last_commit,
         )
     except FileNotFoundError:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
+        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))
 
@@ -880,32 +929,104 @@ async def get_repository_branches(
 
     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,
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found"
         )
-    except RuntimeError as e:
-        logger.error(
-            "Failed to list branches for repo %s: %s",
-            repo_id,
-            str(e),
-            exc_info=True,
-        )
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+    # Try local repo first (.git subdir for normal repos, HEAD for bare)
+    is_valid_git_repo = os.path.isdir(
+        os.path.join(repo.path, ".git")
+    ) or os.path.isfile(os.path.join(repo.path, "HEAD"))
+
+    if is_valid_git_repo:
+        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:
+            logger.error(
+                "Failed to list branches for repo %s: %s",
+                repo_id,
+                str(e),
+                exc_info=True,
+            )
+            raise HTTPException(
+                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e)
+            ) from e
+
+    # Local repo missing/corrupt — try remote if available
+    if repo.remote_url:
+        ssh_key = None
+        if repo.ssh_key_id:
+            ssh_key = await session.get(SSHKey, repo.ssh_key_id)
+
+        ssh_result = _prepare_ssh_env(ssh_key)
+        env = None
+        key_path = None
+        if ssh_result:
+            env, key_path = ssh_result
+
+        try:
+            result = subprocess.run(
+                ["git", "ls-remote", "--heads", repo.remote_url],
+                capture_output=True,
+                text=True,
+                timeout=30,
+                env={**os.environ, **env} if env else None,
+            )
+            if result.returncode == 0:
+                remote_branches = []
+                default_branch = "main"
+                for line in result.stdout.strip().split("\n"):
+                    if line:
+                        parts = line.split("\t")
+                        if len(parts) == 2:
+                            ref = parts[1]
+                            if ref.startswith("refs/heads/"):
+                                branch_name = ref[len("refs/heads/") :]
+                                remote_branches.append(branch_name)
+                                if branch_name in ("main", "master"):
+                                    default_branch = branch_name
+                if remote_branches:
+                    return BranchesResponse(
+                        branches=[
+                            {
+                                "name": b,
+                                "is_default": b == default_branch,
+                                "last_commit": None,
+                            }
+                            for b in remote_branches
+                        ],
+                        default_branch=default_branch,
+                    )
+            else:
+                logger.warning(
+                    "ls-remote returned %d for repo %s: %s",
+                    result.returncode,
+                    repo_id,
+                    result.stderr,
+                )
+        except subprocess.TimeoutExpired:
+            logger.warning("ls-remote timed out for repo %s", repo_id)
+        except Exception as e:
+            logger.warning("ls-remote failed for repo %s: %s", repo_id, str(e))
+        finally:
+            if key_path and os.path.exists(key_path):
+                os.unlink(key_path)
+
+    raise HTTPException(
+        status_code=status.HTTP_404_NOT_FOUND,
+        detail="repository not found on disk — re-clone or re-create the repository",
+    )
 
 
 @router.post(
@@ -938,10 +1059,14 @@ async def update_repository_file(
 
     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")
+        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")
+        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)
@@ -1009,10 +1134,14 @@ async def get_repository_status(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         status_result = get_status(repo.path)
@@ -1068,10 +1197,14 @@ async def create_repository_branch(
 
     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")
+        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")
+        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)
@@ -1111,10 +1244,14 @@ async def delete_repository_branch(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         delete_branch(repo.path, branch_name, force)
@@ -1152,10 +1289,14 @@ async def checkout_repository_branch(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         checkout_branch(repo.path, data.branch)
@@ -1204,10 +1345,14 @@ async def commit_repository_changes(
 
     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")
+        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")
+        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)
@@ -1262,10 +1407,14 @@ async def fetch_repository(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         fetch(repo.path)
@@ -1308,10 +1457,14 @@ async def pull_repository(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         pull(repo.path, branch)
@@ -1354,10 +1507,14 @@ async def push_repository(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         push(repo.path, branch)
@@ -1407,10 +1564,14 @@ async def merge_repository_branches(
 
     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")
+        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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk"
+        )
 
     try:
         commit_hash = merge(

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

@@ -3,42 +3,29 @@ import shutil
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from pydantic import BaseModel, ConfigDict
-from sqlalchemy import select
+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.git_repository import GitRepository
+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.ssh_key import SSHKey
+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"])
 
 
-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,
@@ -76,26 +63,77 @@ async def create_project(
 
 @router.get(
     "",
-    response_model=list[ProjectResponse],
     summary="List all projects",
-    description="Retrieve all projects owned by the authenticated user.",
+    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[Project]:
+) -> list[dict]:
     """List all projects for the authenticated user.
 
-    Args:
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        List of projects owned by the 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))
-    return list(result.scalars().all())
+    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(
@@ -184,7 +222,9 @@ async def delete_project(
     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))
+    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):

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

@@ -5,9 +5,9 @@ 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"])
 

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

@@ -5,10 +5,16 @@ from datetime import datetime, timezone
 from typing import Any
 
 from fastapi import APIRouter
-from pydantic import BaseModel, Field
 from sqlalchemy import text
 
 from src.database import SessionLocal
+from src.schemas.system import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
 
 router = APIRouter()
 
@@ -16,45 +22,6 @@ router = APIRouter()
 _start_time = time.time()
 
 
-class DatabaseHealth(BaseModel):
-    """Database health check result."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
-class DiskHealth(BaseModel):
-    """Disk space health check result."""
-
-    status: str = Field(description="Disk health status", examples=["healthy"])
-    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
-    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
-
-
-class HealthChecks(BaseModel):
-    """Individual health checks."""
-
-    database: DatabaseHealth | None = None
-    disk: DiskHealth | None = None
-
-
-class HealthResponse(BaseModel):
-    """Overall health check response."""
-
-    status: str = Field(description="Overall health status", examples=["healthy"])
-    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
-    version: str = Field(description="API version", examples=["0.1.0"])
-    checks: HealthChecks = Field(description="Individual health checks")
-    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
-
-
-class DatabaseHealthResponse(BaseModel):
-    """Database-specific health check response."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
 @router.get(
     "/health",
     response_model=HealthResponse,

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

@@ -8,8 +8,8 @@ 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.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolInstance
+from src.models import ToolType
 
 logger = logging.getLogger(__name__)
 

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/terminal.py

@@ -1,324 +0,0 @@
-"""WebSocket terminal endpoint for tool instances."""
-
-import asyncio
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.services.terminal_manager import terminal_manager
-
-router = APIRouter()
-logger = logging.getLogger(__name__)
-
-
-class SessionRef:
-    """Mutable reference to a terminal session, allowing updates during reset."""
-
-    def __init__(self, session):
-        self.session = session
-
-
-@router.websocket(
-    "/ws/tool-instances/{instance_id}/terminal",
-)
-async def terminal_websocket(
-    websocket: WebSocket,
-    instance_id: str,
-    db_session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """WebSocket endpoint for terminal access to a tool instance.
-
-    Provides an interactive terminal session inside a running tool instance container.
-    Sessions persist across WebSocket disconnections.
-
-    Args:
-        websocket: The WebSocket connection.
-        instance_id: UUID string of the tool instance.
-        db_session: Database session.
-
-    Returns:
-        None. Communicates via WebSocket messages.
-    """
-    logger.debug("Terminal WebSocket connection attempt for instance %s", instance_id)
-    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)
-
-    # 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)
-
-    # Get or create terminal session
-    try:
-        session = await terminal_manager.get_or_create_session(
-            instance_uuid,
-            instance.container_id,
-            startup_command=startup_command,
-        )
-        logger.debug("Terminal session ready for instance %s (session_id=%s)", instance_id, session.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)
-
-        # Start I/O loops and heartbeat
-        read_task = asyncio.create_task(_read_loop(session_ref, websocket))
-        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(
-            [read_task, write_task, heartbeat_task],
-            return_when=asyncio.FIRST_COMPLETED,
-        )
-        
-        logger.debug("Terminal loop completed for instance %s, done=%s", instance_id, len(done))
-        
-        # Cancel remaining tasks
-        for task in pending:
-            task.cancel()
-
-    except Exception as exc:
-        logger.error("Terminal session error for instance %s: %s", instance_id, str(exc), exc_info=True)
-        await websocket.close(code=4000, reason=f"Error: {exc}")
-    finally:
-        # Detach WebSocket, don't kill session
-        try:
-            if 'session' in locals():
-                await terminal_manager.detach_websocket(session, websocket)
-                logger.debug("WebSocket detached from session for instance %s", instance_id)
-        except Exception:
-            pass
-
-
-async def _read_loop(session_ref: SessionRef, websocket) -> None:
-    """Read output from the container and send to WebSocket."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            data = await session.read_output()
-            if data:
-                try:
-                    await websocket.send_bytes(data)
-                except Exception:
-                    break
-            else:
-                await asyncio.sleep(0.01)
-    except Exception:
-        pass
-
-
-async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
-    """Read input from WebSocket and send to container."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            message = await websocket.receive()
-            if message["type"] == "websocket.receive":
-                if "bytes" in message:
-                    await session.write_input(message["bytes"])
-                elif "text" in message:
-                    text = message["text"]
-                    if text.startswith("{"):
-                        # Control message (JSON)
-                        import 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(f"Received resize message for instance {instance_id}: {cols}x{rows}")
-                                await session.resize(cols, rows)
-                            elif msg_type == "reset":
-                                # Reset terminal session
-                                logger.debug("Resetting terminal session for instance %s", session.instance_id)
-                                await websocket.send_json({"type": "status", "status": "resetting"})
-                                
-                                # Reset the session
-                                new_session = await terminal_manager.reset_session(
-                                    session.instance_id,
-                                    session.container_id,
-                                    startup_command=session.startup_command,
-                                )
-                                
-                                # Update the mutable session reference so read_loop uses the new session
-                                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
-
-
-@router.post(
-    "/projects/{project_id}/repositories/{repo_id}/instances/{instance_id}/terminal/reset",
-    summary="Reset terminal session",
-    description="Reset the terminal session for a tool instance, killing the current shell and starting fresh.",
-)
-async def reset_terminal_session(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Reset the terminal session for an instance.
-
-    Args:
-        project_id: UUID of the project.
-        repo_id: UUID of the repository.
-        instance_id: UUID of the tool instance.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with status message.
-    """
-    # Get instance and verify it exists and is 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.status != "running" or not instance.container_id:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="Instance is not running"
-        )
-
-    # 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 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}"
-        )
-
-
-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

@@ -1,19 +1,23 @@
 import uuid
-from datetime import datetime
 
 from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.api.tool_types_validation import (
+from src.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.tool_type import ToolType
+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"])
 
@@ -29,203 +33,6 @@ async def _require_admin(user: User) -> None:
     pass
 
 
-class ToolTypeCreate(BaseModel):
-    name: str
-    display_name: str
-    description: str | None = None
-    default_port: int = 0
-    definition_type: str = "compose"
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] = []
-    category: str = "other"
-    interface_type: str = "web"
-    requires_port: bool = True
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str) -> str:
-        if v not in ("compose", "dockerfile"):
-            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-        
-        if v is None:
-            raise ValueError("compose_template is required when definition_type is 'compose'")
-        
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        data = info.data
-        if data.get("definition_type") != "dockerfile":
-            return v
-        
-        if v is None:
-            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
-        
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-        
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str) -> str:
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("default_port")
-    @classmethod
-    def validate_default_port(cls, v: int, info) -> int:
-        data = info.data
-        requires_port = data.get("requires_port", True)
-        if not requires_port:
-            return v
-        if v <= 0 or v > 65535:
-            raise ValueError("Port must be between 1 and 65535")
-        return v
-
-    @field_validator("required_variables")
-    @classmethod
-    def validate_required_variables(cls, v: list[str], info) -> list[str]:
-        if not v:
-            return v
-        
-        data = info.data
-        if data.get("definition_type") != "compose":
-            return v
-        
-        template = data.get("compose_template")
-        if not template:
-            return v
-        
-        for var in v:
-            placeholder = f"{{{{{var}}}}}"
-            if placeholder not in template:
-                raise ValueError(f"Required variable '{var}' not found in compose template")
-        
-        return v
-
-    @model_validator(mode="after")
-    def validate_templates(self) -> "ToolTypeCreate":
-        if self.definition_type == "dockerfile" and self.dockerfile_template is None:
-            raise ValueError("dockerfile_template is required when definition_type is 'dockerfile'")
-        if self.definition_type == "compose" and self.compose_template is None:
-            raise ValueError("compose_template is required when definition_type is 'compose'")
-        
-        # Validate that default_port is exposed in compose template (only if requires_port)
-        if self.requires_port and self.definition_type == "compose" and self.compose_template:
-            try:
-                parsed = validate_compose_yaml(self.compose_template)
-            except ValueError:
-                return self
-            
-            if not check_port_exposed(parsed, self.default_port):
-                raise ValueError(f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section.")
-        
-        return self
-
-
-class ToolTypeUpdate(BaseModel):
-    display_name: str | None = None
-    description: str | None = None
-    default_port: int | None = None
-    definition_type: str | None = None
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-    build_context: dict | None = None
-    readiness_probe: dict | None = None
-    startup_command: str | None = None
-    required_variables: list[str] | None = None
-    category: str | None = None
-    interface_type: str | None = None
-    requires_port: bool | None = None
-
-    @field_validator("definition_type")
-    @classmethod
-    def validate_definition_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("compose", "dockerfile"):
-            raise ValueError("definition_type must be 'compose' or 'dockerfile'")
-        return v
-
-    @field_validator("interface_type")
-    @classmethod
-    def validate_interface_type(cls, v: str | None) -> str | None:
-        if v is None:
-            return v
-        if v not in ("web", "terminal"):
-            raise ValueError("interface_type must be 'web' or 'terminal'")
-        return v
-
-    @field_validator("compose_template")
-    @classmethod
-    def validate_compose_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "compose":
-            return v
-
-        validate_compose_yaml(v)
-        return v
-
-    @field_validator("dockerfile_template")
-    @classmethod
-    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
-        if v is None:
-            return v
-        
-        data = info.data
-        definition_type = data.get("definition_type")
-        if definition_type and definition_type != "dockerfile":
-            return v
-        
-        if not v.strip().startswith("FROM"):
-            raise ValueError("Dockerfile must start with a FROM instruction")
-        
-        return v
-
-
-class ToolTypeResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    display_name: str
-    description: str | None
-    category: str
-    interface_type: str
-    requires_port: bool
-    default_port: int
-    definition_type: str
-    compose_template: str | None
-    dockerfile_template: str | None
-    build_context: dict | None
-    readiness_probe: dict | None
-    startup_command: str | None
-    required_variables: list[str]
-    created_by_id: uuid.UUID | None
-    created_at: datetime
-    updated_at: datetime
-
-
 @router.post(
     "",
     response_model=ToolTypeResponse,
@@ -250,18 +57,22 @@ async def create_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")
-    
+        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,
@@ -327,7 +138,9 @@ async def get_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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
     return tool_type
 
 
@@ -356,15 +169,17 @@ async def update_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")
-    
+        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:
@@ -372,9 +187,9 @@ async def update_tool_type(
         if new_port <= 0 or new_port > 65535:
             raise HTTPException(
                 status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Port must be between 1 and 65535"
+                detail="Port must be between 1 and 65535",
             )
-        
+
         # Only validate port exposure for compose definitions
         definition_type = update_data.get("definition_type", tool_type.definition_type)
         if definition_type == "compose":
@@ -385,12 +200,11 @@ async def update_tool_type(
                     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"
+                            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)
+                        status_code=status.HTTP_400_BAD_REQUEST, detail=str(e)
                     )
 
     # Validate required variables for compose definitions
@@ -404,21 +218,22 @@ async def update_tool_type(
             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
 
 
-class ToolTypeValidateRequest(BaseModel):
-    definition_type: str
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-
-
 @router.post(
     "/validate",
     summary="Validate tool type template",
@@ -458,8 +273,11 @@ async def validate_tool_type_template(
         elif not data.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
 
+    elif data.definition_type == "manifest":
+        pass  # Manifest validation is handled separately
+
     else:
-        errors.append("definition_type must be 'compose' or 'dockerfile'")
+        errors.append("definition_type must be 'compose', 'dockerfile', or 'manifest'")
 
     return {
         "valid": len(errors) == 0,
@@ -490,10 +308,12 @@ async def validate_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")
-    
+        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")
@@ -502,13 +322,17 @@ async def validate_tool_type(
                 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,
@@ -538,12 +362,14 @@ async def delete_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")
-    
+        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_configs.py

@@ -1,290 +0,0 @@
-"""Tool configuration API endpoints."""
-
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, Field, field_validator
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.api.shared_validators import validate_env_vars as _validate_env_vars, validate_volumes as _validate_volumes
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_config import ToolConfig
-from src.models.tool_type import ToolType
-
-router = APIRouter(prefix="/tool-configs", tags=["tool-configs"])
-
-
-class ToolConfigCreate(BaseModel):
-    tool_type_id: str = Field(description="UUID of the tool type")
-    project_id: str | None = Field(default=None, description="Optional project ID for project-scoped config")
-    key: str = Field(description="Config key name")
-    value: str = Field(description="Config value")
-    config_type: str = Field(default="env", description="Type: env or file")
-    file_path: str | None = Field(default=None, description="File path for file-type configs")
-    port_override: int | None = Field(default=None, description="Port override (1-65535)")
-    start_command: str | None = Field(default=None, description="Override container start command")
-    working_directory: str | None = Field(default=None, description="Working directory inside container")
-    environment_variables: dict | None = Field(default=None, description="Environment variables as JSON object")
-    volumes: list[dict] | None = Field(default=None, description="Volume mounts as JSON array")
-
-    @field_validator("port_override")
-    @classmethod
-    def validate_port(cls, v: int | None) -> int | None:
-        if v is None:
-            return v
-        if v < 1 or v > 65535:
-            raise ValueError("Port must be between 1 and 65535")
-        return v
-
-    @field_validator("environment_variables")
-    @classmethod
-    def validate_env_vars(cls, v: dict | None) -> dict | None:
-        return _validate_env_vars(v)
-
-    @field_validator("volumes")
-    @classmethod
-    def validate_volumes(cls, v: list | None) -> list | None:
-        return _validate_volumes(v)
-
-
-class ToolConfigUpdate(BaseModel):
-    key: str | None = Field(default=None, description="Config key name")
-    value: str | None = Field(default=None, description="Config value")
-    config_type: str | None = Field(default=None, description="Type: env or file")
-    file_path: str | None = Field(default=None, description="File path for file-type configs")
-    port_override: int | None = Field(default=None, description="Port override (1-65535)")
-    start_command: str | None = Field(default=None, description="Override container start command")
-    working_directory: str | None = Field(default=None, description="Working directory inside container")
-    environment_variables: dict | None = Field(default=None, description="Environment variables as JSON object")
-    volumes: list[dict] | None = Field(default=None, description="Volume mounts as JSON array")
-
-    @field_validator("port_override")
-    @classmethod
-    def validate_port(cls, v: int | None) -> int | None:
-        if v is None:
-            return v
-        if v < 1 or v > 65535:
-            raise ValueError("Port must be between 1 and 65535")
-        return v
-
-    @field_validator("environment_variables")
-    @classmethod
-    def validate_env_vars(cls, v: dict | None) -> dict | None:
-        return _validate_env_vars(v)
-
-    @field_validator("volumes")
-    @classmethod
-    def validate_volumes(cls, v: list | None) -> list | None:
-        return _validate_volumes(v)
-
-
-class ToolConfigResponse(BaseModel):
-    id: str
-    tool_type_id: str
-    project_id: str | None
-    key: str
-    value: str
-    config_type: str
-    file_path: str | None
-    port_override: int | None
-    start_command: str | None
-    working_directory: str | None
-    environment_variables: dict | None
-    volumes: list[dict] | None
-
-
-@router.get("", summary="List tool configs", description="Get all tool configs for the current user.")
-async def list_configs(
-    tool_type_id: str | None = None,
-    project_id: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> list:
-    """List tool configs for the current user."""
-    query = select(ToolConfig).where(ToolConfig.user_id == user_id)
-    
-    if tool_type_id:
-        query = query.where(ToolConfig.tool_type_id == uuid.UUID(tool_type_id))
-    if project_id:
-        query = query.where(ToolConfig.project_id == uuid.UUID(project_id))
-    else:
-        # If no project specified, get only global configs (project_id is None)
-        query = query.where(ToolConfig.project_id.is_(None))
-    
-    result = await session.execute(query)
-    configs = result.scalars().all()
-    
-    return [
-        {
-            "id": str(c.id),
-            "tool_type_id": str(c.tool_type_id),
-            "project_id": str(c.project_id) if c.project_id else None,
-            "key": c.key,
-            "value": c.value,
-            "config_type": c.config_type,
-            "file_path": c.file_path,
-            "port_override": c.port_override,
-            "start_command": c.start_command,
-            "working_directory": c.working_directory,
-            "environment_variables": c.environment_variables,
-            "volumes": c.volumes,
-        }
-        for c in configs
-    ]
-
-
-@router.post("", summary="Create tool config", description="Create a new tool config.", status_code=status.HTTP_201_CREATED)
-async def create_config(
-    data: ToolConfigCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a tool config."""
-    # Verify tool type exists
-    tool_type = await session.get(ToolType, uuid.UUID(data.tool_type_id))
-    if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    # Check for existing config with same key
-    query = select(ToolConfig).where(
-        ToolConfig.user_id == user_id,
-        ToolConfig.tool_type_id == uuid.UUID(data.tool_type_id),
-        ToolConfig.key == data.key,
-    )
-    if data.project_id:
-        query = query.where(ToolConfig.project_id == uuid.UUID(data.project_id))
-    else:
-        query = query.where(ToolConfig.project_id.is_(None))
-    
-    existing = await session.scalar(query)
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"config with key '{data.key}' already exists"
-        )
-    
-    config = ToolConfig(
-        user_id=user_id,
-        tool_type_id=uuid.UUID(data.tool_type_id),
-        project_id=uuid.UUID(data.project_id) if data.project_id else None,
-        key=data.key,
-        value=data.value,
-        config_type=data.config_type,
-        file_path=data.file_path,
-        port_override=data.port_override,
-        start_command=data.start_command,
-        working_directory=data.working_directory,
-        environment_variables=data.environment_variables,
-        volumes=data.volumes,
-    )
-    session.add(config)
-    await session.commit()
-    await session.refresh(config)
-    
-    return {
-        "id": str(config.id),
-        "tool_type_id": str(config.tool_type_id),
-        "project_id": str(config.project_id) if config.project_id else None,
-        "key": config.key,
-        "value": config.value,
-        "config_type": config.config_type,
-        "file_path": config.file_path,
-        "port_override": config.port_override,
-        "start_command": config.start_command,
-        "working_directory": config.working_directory,
-        "environment_variables": config.environment_variables,
-        "volumes": config.volumes,
-    }
-
-
-@router.put("/{config_id}", summary="Update tool config", description="Update an existing tool config.")
-async def update_config(
-    config_id: uuid.UUID,
-    data: ToolConfigUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a tool config."""
-    config = await session.get(ToolConfig, config_id)
-    if config is None or config.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
-    
-    if data.key is not None:
-        config.key = data.key
-    if data.value is not None:
-        config.value = data.value
-    if data.config_type is not None:
-        config.config_type = data.config_type
-    if data.file_path is not None:
-        config.file_path = data.file_path
-    if data.port_override is not None:
-        config.port_override = data.port_override
-    if data.start_command is not None:
-        config.start_command = data.start_command
-    if data.working_directory is not None:
-        config.working_directory = data.working_directory
-    if data.environment_variables is not None:
-        config.environment_variables = data.environment_variables
-    if data.volumes is not None:
-        config.volumes = data.volumes
-    
-    await session.commit()
-    await session.refresh(config)
-    
-    return {
-        "id": str(config.id),
-        "tool_type_id": str(config.tool_type_id),
-        "project_id": str(config.project_id) if config.project_id else None,
-        "key": config.key,
-        "value": config.value,
-        "config_type": config.config_type,
-        "file_path": config.file_path,
-        "port_override": config.port_override,
-        "start_command": config.start_command,
-        "working_directory": config.working_directory,
-        "environment_variables": config.environment_variables,
-        "volumes": config.volumes,
-    }
-
-
-@router.get("/defaults/{tool_type_id}", summary="Get default configs", description="Get suggested default configs for a tool type.")
-async def get_default_configs(
-    tool_type_id: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get suggested default configs for a tool type."""
-    tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
-    if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    # Return suggested defaults based on required_variables
-    defaults = []
-    for var in tool_type.required_variables:
-        defaults.append({
-            "key": var,
-            "value": "",
-            "config_type": "env",
-            "description": f"Required variable: {var}",
-        })
-    
-    return {
-        "tool_type_id": tool_type_id,
-        "suggested_configs": defaults,
-    }
-
-
-@router.delete("/{config_id}", summary="Delete tool config", description="Delete a tool config.")
-async def delete_config(
-    config_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a tool config."""
-    config = await session.get(ToolConfig, config_id)
-    if config is None or config.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config not found")
-    
-    await session.delete(config)
-    await session.commit()

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

@@ -1,18 +1,24 @@
 import base64
 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_user, get_current_user_id, get_db_session
 from src.config import Settings
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
+from src.schemas.project import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 
@@ -21,7 +27,7 @@ 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()
@@ -53,36 +59,6 @@ def generate_ssh_key_pair() -> tuple[str, str]:
     return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
 
 
-class SSHKeyCreate(BaseModel):
-    name: str
-
-
-class SSHKeyResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    public_key: str
-    created_at: datetime
-
-
-class SignPayloadRequest(BaseModel):
-    payload: str
-
-
-class SignatureResponse(BaseModel):
-    signature: str
-
-
-class VerifySignatureRequest(BaseModel):
-    payload: str
-    signature: str
-
-
-class VerifySignatureResponse(BaseModel):
-    valid: bool
-
-
 @router.post(
     "",
     response_model=SSHKeyResponse,
@@ -171,7 +147,9 @@ async def delete_ssh_key(
     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")
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
+        )
 
     await session.delete(ssh_key)
     await session.commit()
@@ -203,7 +181,9 @@ async def sign_payload(
     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")
+        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()
@@ -242,7 +222,9 @@ async def verify_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")
+        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())
 

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_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"])
 
@@ -16,20 +16,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-class UserProfileResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    email: str
-    name: str
-    avatar_url: str | None
-
-
-class UserProfileUpdate(BaseModel):
-    name: str | None = None
-    email: str | None = None
-
-
 @router.get(
     "/me",
     response_model=UserProfileResponse,
@@ -77,12 +63,16 @@ async def update_profile(
 
     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()

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/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

@@ -7,29 +7,42 @@ from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
 
-from src.api.auth import router as auth_router
-from src.api.dashboard import router as dashboard_router
-from src.api.git_repositories import router as git_repositories_router
-from src.api.health import router as health_router
-from src.api.projects import router as projects_router
-from src.api.ssh_keys import router as ssh_keys_router
-from src.api.terminal import router as terminal_router
-from src.api.instance_proxy import router as instance_proxy_router
-from src.api.config_folders import router as config_folders_router
-from src.api.config_profiles import router as config_profiles_router
-from src.api.tool_configs import router as tool_configs_router
-from src.api.tool_instances import router as tool_instances_router
-from src.api.tool_instances import sessions_router
-from src.api.tool_types import router as tool_types_router
-from src.api.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.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.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()
@@ -54,6 +67,7 @@ app.add_middleware(
     allow_headers=["*"],
 )
 
+app.add_middleware(CorrelationIdMiddleware)
 app.add_middleware(RequestLoggingMiddleware)
 app.add_middleware(ExceptionLoggingMiddleware)
 
@@ -66,7 +80,9 @@ def _sanitize_validation_errors(errors):
             "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,
+            "input": str(error.get("input"))
+            if error.get("input") is not None
+            else None,
         }
         # Convert ctx to safe format
         ctx = error.get("ctx")
@@ -101,6 +117,11 @@ async def validation_exception_handler(request: Request, exc: RequestValidationE
     )
 
 
+# Global services
+_event_bus = InstanceEventBus()
+_health_monitor = HealthMonitor(_event_bus)
+
+
 @app.on_event("startup")
 async def on_startup():
     logger.info("Starting up Headquarter API...")
@@ -110,10 +131,28 @@ async def on_startup():
     if not db_ready:
         logger.error("Database initialization failed. Shutting down.")
         import sys
+
         sys.exit(1)
 
+    # 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.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)
@@ -123,11 +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(config_folders_router)
+app.include_router(tool_definitions_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
-app.include_router(tool_configs_router)
 app.include_router(sessions_router)
 app.include_router(instance_proxy_router)
 app.include_router(terminal_router)
+app.include_router(events_router)
+app.include_router(notifications_router)
+app.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

@@ -1,12 +1,34 @@
 from src.models.base import Base
-from src.models.config_folder import ConfigFolder
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
-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", "ConfigFolder", "ConfigProfile", "ConfigProfileInclude", "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

@@ -1,7 +1,15 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import ForeignKey, JSON, Integer, String, Text, Boolean
+from sqlalchemy import (
+    Boolean,
+    ForeignKey,
+    JSON,
+    Integer,
+    String,
+    Text,
+    UniqueConstraint,
+)
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
@@ -9,12 +17,15 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.tool_type import ToolType
+    from src.models 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

apps/api/src/models/config_folder.py

@@ -1,31 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class ConfigFolder(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "config_folders"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
-    )
-    name: Mapped[str] = mapped_column(String(255), nullable=False)
-    description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    mount_path: Mapped[str] = mapped_column(String(1024), nullable=False)
-    files: Mapped[dict] = mapped_column(
-        JSON, default=dict, nullable=False
-    )  # {"relative/path": "content", ...}
-    project_overrides: Mapped[dict | None] = mapped_column(
-        JSON, default=dict, nullable=True
-    )  # {"project_id": {"mount_path": "...", "files": {...}}}
-    is_active: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
-
-    user: Mapped["User"] = relationship()

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

@@ -10,7 +10,7 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.ssh_key import SSHKey
+    from src.models import SSHKey
     from src.models.user import User
 
 

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

@@ -8,8 +8,8 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
-    from src.models.git_repository import GitRepository
-    from src.models.ssh_key import SSHKey
+    from src.models import GitRepository
+    from src.models import SSHKey
     from src.models.user import User
 
 

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

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

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

@@ -0,0 +1,8 @@
+"""System models module."""
+
+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
+
+__all__ = ["HealthCheck", "InstanceEvent", "Notification", "TerminalSessionModel"]

apps/api/src/models/system/health_check.py

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

apps/api/src/models/system/instance_event.py

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

apps/api/src/models/system/notification.py

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

apps/api/src/models/system/terminal_session.py

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

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

@@ -0,0 +1,7 @@
+"""Tool models module."""
+
+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
+
+__all__ = ["ToolDefinitionManifest", "ToolInstance", "ToolType"]

apps/api/src/models/tool/tool_definition_manifest.py

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

apps/api/src/models/tool/tool_instance.py

@@ -9,11 +9,12 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
-    from src.models.config_profile import ConfigProfile
-    from src.models.git_repository import GitRepository
+    from src.models import ConfigProfile
+    from src.models import GitRepository
     from src.models.project import Project
-    from src.models.tool_type import ToolType
+    from src.models import ToolType
     from src.models.user import User
+    from src.models import Workspace
 
 
 class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
@@ -33,50 +34,39 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     owner_id: Mapped[uuid.UUID] = mapped_column(
         UUID(), ForeignKey("users.id"), nullable=False
     )
-    status: Mapped[str] = mapped_column(
-        String(50), nullable=False, default="pending"
-    )
-    container_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    container_name: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    compose_path: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    public_url: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )
-    tunnel_id: Mapped[str | None] = mapped_column(
-        String(255), nullable=True
-    )
-    port: Mapped[int | None] = mapped_column(
-        Integer, nullable=True
-    )
+    status: Mapped[str] = mapped_column(String(50), nullable=False, default="pending")
+    container_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    container_name: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    compose_path: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    public_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    tunnel_id: Mapped[str | None] = mapped_column(String(255), nullable=True)
+    port: Mapped[int | None] = mapped_column(Integer, nullable=True)
     last_started_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
     last_stopped_at: Mapped[datetime | None] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
-    probe_result: Mapped[dict | None] = mapped_column(
-        JSON, nullable=True
-    )
-    clone_mode: Mapped[str] = mapped_column(
-        String(20), nullable=False, default="mount"
+    manifest_compiled_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
     )
+    image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
+    probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
+    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
     branch: Mapped[str | None] = mapped_column(
         String(255), nullable=True, default="main"
     )
     selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
     )
+    ssh_key_ids: Mapped[list[str] | None] = mapped_column(JSON, nullable=True)
+    workspace_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("workspaces.id", ondelete="SET NULL"), nullable=True
+    )
 
     tool_type: Mapped["ToolType"] = relationship()
+    workspace: Mapped["Workspace | None"] = relationship()
     repository: Mapped["GitRepository"] = relationship()
     project: Mapped["Project"] = relationship()
     owner: Mapped["User"] = relationship()

apps/api/src/models/tool/tool_type.py

@@ -6,6 +6,7 @@ from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
 
 if TYPE_CHECKING:
     from src.models.user import User
@@ -18,12 +19,19 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     display_name: Mapped[str] = mapped_column(String(255), nullable=False)
     description: Mapped[str | None] = mapped_column(Text, nullable=True)
     category: Mapped[str] = mapped_column(String(50), nullable=False, default="other")
-    interface_type: Mapped[str] = mapped_column(String(20), nullable=False, default="web")
+    interface_type: Mapped[str] = mapped_column(
+        String(20), nullable=False, default="web"
+    )
     requires_port: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
     default_port: Mapped[int] = mapped_column(nullable=False)
     definition_type: Mapped[str] = mapped_column(
-        String(20), nullable=False, default="compose"
-    )  # "compose" or "dockerfile"
+        String(16), nullable=False, default="legacy"
+    )  # "legacy" | "manifest"
+    manifest_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(),
+        ForeignKey("tool_definition_manifests.id"),
+        nullable=True,
+    )
     compose_template: Mapped[str | None] = mapped_column(Text, nullable=True)
     dockerfile_template: Mapped[str | None] = mapped_column(Text, nullable=True)
     build_context: Mapped[dict | None] = mapped_column(
@@ -31,11 +39,16 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     )
     readiness_probe: Mapped[dict | None] = mapped_column(JSON, nullable=True)
     startup_command: Mapped[str | None] = mapped_column(Text, nullable=True)
-    required_variables: Mapped[list[str]] = mapped_column(JSON, default=list, nullable=False)
+    required_variables: Mapped[list[str]] = mapped_column(
+        JSON, default=list, nullable=False
+    )
     created_by_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(),
         ForeignKey("users.id"),
         nullable=True,
     )
 
+    manifest: Mapped["ToolDefinitionManifest | None"] = relationship(
+        foreign_keys=[manifest_id],
+    )
     created_by: Mapped["User | None"] = relationship()

apps/api/src/models/tool_config.py

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

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

@@ -0,0 +1,7 @@
+"""User models module."""
+
+from src.models.user.ssh_key import SSHKey
+from src.models.user.user import User
+from src.models.user.user_config import UserConfig
+
+__all__ = ["SSHKey", "User", "UserConfig"]

apps/api/src/models/user/user.py

@@ -7,8 +7,8 @@ from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
 if TYPE_CHECKING:
     from src.models.project import Project
-    from src.models.ssh_key import SSHKey
-    from src.models.user_config import UserConfig
+    from src.models import SSHKey
+    from src.models import UserConfig
 
 
 class User(UUIDPrimaryKeyMixin, TimestampMixin, Base):

apps/api/src/models/user/user_config.py

@@ -0,0 +1,51 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, JSON
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.user import User
+
+
+class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "user_configs"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(), ForeignKey("users.id"), nullable=False, unique=True
+    )
+    config: Mapped[dict[str, object]] = mapped_column(
+        JSON, default=dict, nullable=False
+    )
+
+    user: Mapped["User"] = relationship(back_populates="user_config")
+
+    @property
+    def default_profile_id(self) -> uuid.UUID | None:
+        """Return the legacy global default profile ID from config JSON."""
+        profile_id = self.config.get("default_profile_id")
+        if isinstance(profile_id, str):
+            return uuid.UUID(profile_id)
+        return None
+
+    @default_profile_id.setter
+    def default_profile_id(self, value: uuid.UUID | None) -> None:
+        if value is not None:
+            self.config["default_profile_id"] = str(value)
+        elif "default_profile_id" in self.config:
+            del self.config["default_profile_id"]
+
+    @property
+    def default_profiles(self) -> dict[str, str]:
+        """Return per-tool-type default profile IDs from config JSON."""
+        value = self.config.get("default_profiles", {})
+        if isinstance(value, dict):
+            return {str(k): str(v) for k, v in value.items()}
+        return {}
+
+    @default_profiles.setter
+    def default_profiles(self, value: dict[str, str]) -> None:
+        self.config["default_profiles"] = value

apps/api/src/models/user_config.py

@@ -1,20 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey
-from sqlalchemy import JSON, Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class UserConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "user_configs"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False, unique=True)
-    config: Mapped[dict[str, object]] = mapped_column(JSON, default=dict, nullable=False)
-
-    user: Mapped["User"] = relationship(back_populates="user_config")

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

@@ -0,0 +1,27 @@
+"""Config schemas module."""
+
+from src.schemas.config.config_profile import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    GitMountItem,
+    GitMountMapping,
+    MountItem,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+
+__all__ = [
+    "ConfigProfileCreate",
+    "ConfigProfileIncludeUpdate",
+    "ConfigProfileResponse",
+    "ConfigProfileUpdate",
+    "DefaultProfilesUpdate",
+    "GitMountItem",
+    "GitMountMapping",
+    "MountItem",
+    "ValidateGitUrlRequest",
+    "ValidateGitUrlResponse",
+]

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

@@ -0,0 +1,280 @@
+"""Config profile request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, Field, field_validator, model_validator
+
+from src.api.shared_validators import validate_env_vars as _validate_env_vars
+
+
+def _validate_uuid(v: str | None) -> str | None:
+    if v is None:
+        return v
+    try:
+        uuid.UUID(v)
+    except ValueError as exc:
+        raise ValueError(f"Invalid UUID: {v}") from exc
+    return v
+
+
+class GitMountMapping(BaseModel):
+    source_path: str = Field(
+        description="Path within repository (supports glob patterns)"
+    )
+    target_path: str = Field(description="Absolute path inside container")
+
+    @field_validator("source_path")
+    @classmethod
+    def validate_source_path(cls, v: str) -> str:
+        if v.startswith("/"):
+            raise ValueError("source_path must be relative (no leading /)")
+        if ".." in v:
+            raise ValueError("source_path cannot contain path traversal (..)")
+        return v
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str) -> str:
+        if ".." in v:
+            raise ValueError("target_path cannot contain path traversal (..)")
+        return v
+
+
+class GitMountItem(BaseModel):
+    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
+    source_path: str | None = Field(
+        default=None, description="Path within repository (legacy single mapping)"
+    )
+    target_path: str | None = Field(
+        default=None,
+        description="Absolute path inside container (legacy single mapping)",
+    )
+    branch: str | None = Field(default=None, description="Optional branch or tag name")
+    mappings: list[GitMountMapping] | None = Field(
+        default=None, description="Multiple source/target mappings from the same repo"
+    )
+
+    @field_validator("remote_url")
+    @classmethod
+    def validate_remote_url(cls, v: str) -> str:
+        if not v.startswith(("http://", "https://", "git@", "ssh://")):
+            raise ValueError(
+                "remote_url must be a valid git URL (https://, git@, or ssh://)"
+            )
+        return v
+
+    @field_validator("source_path")
+    @classmethod
+    def validate_source_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v.startswith("/"):
+            raise ValueError("source_path must be relative (no leading /)")
+        if ".." in v:
+            raise ValueError("source_path cannot contain path traversal (..)")
+        return v
+
+    @field_validator("target_path")
+    @classmethod
+    def validate_target_path(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if ".." in v:
+            raise ValueError("target_path cannot contain path traversal (..)")
+        return v
+
+    @model_validator(mode="after")
+    def check_mappings_or_legacy(self):
+        has_legacy = self.source_path is not None and self.target_path is not None
+        has_mappings = self.mappings is not None and len(self.mappings) > 0
+        if not has_legacy and not has_mappings:
+            raise ValueError(
+                "Git mount must have either 'mappings' (non-empty array) or both 'source_path' and 'target_path'"
+            )
+        return self
+
+
+class MountItem(BaseModel):
+    target: str = Field(description="Absolute mount target path")
+    mode: str = Field(default="rw", description="Mount mode: ro or rw")
+    files: dict = Field(
+        default_factory=dict, description="Files as {relative_path: content}"
+    )
+
+    @field_validator("target")
+    @classmethod
+    def validate_target(cls, v: str) -> str:
+        if not v.startswith("/"):
+            raise ValueError("Mount target must be absolute (start with /)")
+        return v
+
+    @field_validator("mode")
+    @classmethod
+    def validate_mode(cls, v: str) -> str:
+        if v not in ("ro", "rw"):
+            raise ValueError("Mount mode must be 'ro' or 'rw'")
+        return v
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v:
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"Mount file paths must be relative (got: {path}). "
+                    f"The mount target defines the absolute container path."
+                )
+        return v
+
+
+class ConfigProfileCreate(BaseModel):
+    name: str = Field(description="Profile name (unique per user)")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict = Field(default_factory=dict, description="Environment variables")
+    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
+    mounts: list[MountItem] = Field(
+        default_factory=list, description="Mount definitions"
+    )
+    files: dict = Field(
+        default_factory=dict, description="Files as {relative_path: content}"
+    )
+    git_mounts: list[GitMountItem] = Field(
+        default_factory=list, description="Git repository mounts"
+    )
+    is_default: bool = Field(
+        default=False, description="Whether this is the default profile for its scope"
+    )
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict) -> dict:
+        for path in v:
+            if ".." in path or not path:
+                raise ValueError(f"Invalid file path: {path}")
+            if path.startswith("/"):
+                raise ValueError(
+                    f"File paths must be relative (got: {path}). "
+                    f"Use Mounts for absolute container paths."
+                )
+        return v
+
+    @field_validator("env_vars")
+    @classmethod
+    def validate_env_vars(cls, v: dict) -> dict:
+        result = _validate_env_vars(v)
+        if result is None:
+            raise ValueError("env_vars must be a JSON object")
+        return result
+
+    @field_validator("runtime_hints")
+    @classmethod
+    def validate_runtime_hints(cls, v: dict) -> dict:
+        if not isinstance(v, dict):
+            raise ValueError("runtime_hints must be a JSON object")
+        return v
+
+    @field_validator("mounts")
+    @classmethod
+    def validate_mounts(cls, v: list) -> list:
+        if not isinstance(v, list):
+            raise ValueError("mounts must be a JSON array")
+        return v
+
+
+class ConfigProfileUpdate(BaseModel):
+    name: str | None = Field(default=None, description="Profile name")
+    description: str | None = Field(default=None, description="Optional description")
+    project_id: str | None = Field(default=None, description="Optional project ID")
+    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
+    env_vars: dict | None = Field(default=None, description="Environment variables")
+    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
+    mounts: list[MountItem] | None = Field(
+        default=None, description="Mount definitions"
+    )
+    files: dict | None = Field(
+        default=None, description="Files as {relative_path: content}"
+    )
+    git_mounts: list[GitMountItem] | None = Field(
+        default=None, description="Git repository mounts"
+    )
+    is_default: bool | None = Field(
+        default=None, description="Whether this is the default profile"
+    )
+
+    @field_validator("project_id", "tool_type_id")
+    @classmethod
+    def validate_uuids(cls, v: str | None) -> str | None:
+        return _validate_uuid(v)
+
+    @field_validator("files")
+    @classmethod
+    def validate_files(cls, v: dict | None) -> dict | None:
+        if v is None:
+            return v
+        for path in v:
+            if ".." in path or path.startswith("/") or not path:
+                raise ValueError(f"Invalid file path: {path}")
+        return v
+
+
+class ConfigProfileIncludeUpdate(BaseModel):
+    includes: list[str] = Field(description="Ordered list of included profile IDs")
+
+    @field_validator("includes")
+    @classmethod
+    def validate_includes(cls, v: list) -> list:
+        for item in v:
+            try:
+                uuid.UUID(item)
+            except ValueError as exc:
+                raise ValueError(f"Invalid UUID in includes: {item}") from exc
+        return v
+
+
+class ConfigProfileResponse(BaseModel):
+    id: str
+    user_id: str
+    name: str
+    description: str | None
+    project_id: str | None
+    tool_type_id: str | None
+    env_vars: dict
+    runtime_hints: dict
+    mounts: list
+    files: dict
+    git_mounts: list
+    is_default: bool
+    includes: list[dict]
+    created_at: str
+    updated_at: str
+
+
+class DefaultProfilesUpdate(BaseModel):
+    default_profiles: dict[str, str] = Field(
+        description="Mapping of tool_type_id -> profile_id for default profiles"
+    )
+
+
+class ValidateGitUrlRequest(BaseModel):
+    url: str = Field(description="Git remote URL to validate")
+    ssh_key_id: str | None = Field(
+        default=None, description="Optional SSH key ID for private repos"
+    )
+
+
+class ValidateGitUrlResponse(BaseModel):
+    valid: bool
+    suggested_url: str | None = None
+    branches: list[str] | None = None
+    default_branch: str | None = None
+    error: str | None = None
+    error_code: str | None = None

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

@@ -0,0 +1,41 @@
+"""Project schemas module."""
+
+from src.schemas.project.git_repository import (
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    UpdateSSHKeyRequest,
+    URLParseRequest,
+    URLParseResponse,
+)
+from src.schemas.project.project import (
+    ProjectCreate,
+    ProjectResponse,
+    ProjectUpdate,
+    SetDefaultSSHKeyRequest,
+)
+from src.schemas.project.ssh_key import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)
+
+__all__ = [
+    "GitRepositoryCreate",
+    "GitRepositoryResponse",
+    "ProjectCreate",
+    "ProjectResponse",
+    "ProjectUpdate",
+    "SSHKeyCreate",
+    "SSHKeyResponse",
+    "SetDefaultSSHKeyRequest",
+    "SignPayloadRequest",
+    "SignatureResponse",
+    "URLParseRequest",
+    "URLParseResponse",
+    "UpdateSSHKeyRequest",
+    "VerifySignatureRequest",
+    "VerifySignatureResponse",
+]

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

@@ -0,0 +1,47 @@
+"""Git repository request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict
+
+
+class GitRepositoryCreate(BaseModel):
+    name: str
+    remote_url: str | None = None
+    force_original_url: bool = False
+    ssh_key_id: str | None = None
+
+
+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 | None
+    owner_id: uuid.UUID
+    is_mirror: bool
+    remote_url: str | None
+    last_push: datetime | None
+    ssh_key_id: uuid.UUID | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class UpdateSSHKeyRequest(BaseModel):
+    ssh_key_id: str | None = None

apps/api/src/schemas/project/project.py

@@ -0,0 +1,29 @@
+"""Project request/response schemas."""
+
+import uuid
+
+from pydantic import BaseModel, ConfigDict
+
+
+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

apps/api/src/schemas/project/ssh_key.py

@@ -0,0 +1,36 @@
+"""SSH key request/response schemas."""
+
+import uuid
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict
+
+
+class SSHKeyCreate(BaseModel):
+    name: str
+
+
+class SSHKeyResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    public_key: str
+    created_at: datetime
+
+
+class SignPayloadRequest(BaseModel):
+    payload: str
+
+
+class SignatureResponse(BaseModel):
+    signature: str
+
+
+class VerifySignatureRequest(BaseModel):
+    payload: str
+    signature: str
+
+
+class VerifySignatureResponse(BaseModel):
+    valid: bool

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

@@ -0,0 +1,17 @@
+"""System schemas module."""
+
+from src.schemas.system.health import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
+
+__all__ = [
+    "DatabaseHealth",
+    "DatabaseHealthResponse",
+    "DiskHealth",
+    "HealthChecks",
+    "HealthResponse",
+]

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

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

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

@@ -0,0 +1,18 @@
+"""Tool schemas module."""
+
+from src.schemas.tool.tool_instance import CreateInstanceRequest, StartInstanceRequest
+from src.schemas.tool.tool_type import (
+    ToolTypeCreate,
+    ToolTypeResponse,
+    ToolTypeUpdate,
+    ToolTypeValidateRequest,
+)
+
+__all__ = [
+    "CreateInstanceRequest",
+    "StartInstanceRequest",
+    "ToolTypeCreate",
+    "ToolTypeResponse",
+    "ToolTypeUpdate",
+    "ToolTypeValidateRequest",
+]

apps/api/src/schemas/tool/tool_instance.py

@@ -0,0 +1,45 @@
+"""Tool instance request/response schemas."""
+
+from pydantic import BaseModel, Field
+
+
+class CreateInstanceRequest(BaseModel):
+    """Request body for creating a tool instance."""
+
+    model_config = {"extra": "ignore"}
+
+    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
+    display_name: str | None = Field(
+        default=None, description="Optional display name for the instance"
+    )
+    workspace_id: str | None = Field(
+        default=None, description="UUID of workspace to mount (replaces clone_mode)"
+    )
+    clone_mode: str = Field(
+        default="mount", description="Repository access mode: 'mount' or 'clone'"
+    )
+    branch: str | None = Field(
+        default="main", description="Branch to clone (when clone_mode='clone')"
+    )
+    new_branch: str | None = Field(
+        default=None, description="Create a new local branch after cloning"
+    )
+    config_profile_id: str | None = Field(
+        default=None, description="Optional config profile ID for launch"
+    )
+    ssh_key_ids: list[str] = Field(
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
+    )
+
+
+class StartInstanceRequest(BaseModel):
+    """Request body for starting a tool instance."""
+
+    model_config = {"extra": "ignore"}
+
+    config_profile_id: str | None = Field(
+        default=None, description="Config profile ID to apply, or null for none"
+    )
+    ssh_key_ids: list[str] = Field(
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
+    )

apps/api/src/schemas/tool/tool_type.py

@@ -0,0 +1,230 @@
+"""Tool type request/response schemas."""
+
+import uuid
+
+from datetime import datetime
+
+from pydantic import BaseModel, ConfigDict, field_validator, model_validator
+
+from src.api.tool.tool_types_validation import (
+    check_port_exposed,
+    validate_compose_yaml,
+    validate_required_variables,
+)
+
+
+class ToolTypeCreate(BaseModel):
+    name: str
+    display_name: str
+    description: str | None = None
+    default_port: int = 0
+    definition_type: str = "compose"
+    manifest_id: uuid.UUID | None = None
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    startup_command: str | None = None
+    required_variables: list[str] = []
+    category: str = "other"
+    interface_type: str = "web"
+    requires_port: bool = True
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str) -> str:
+        if v not in ("compose", "dockerfile", "manifest"):
+            raise ValueError(
+                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
+            )
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+
+        if v is None or not v.strip():
+            raise ValueError(
+                "compose_template is required when definition_type is 'compose'"
+            )
+
+        validate_compose_yaml(v)
+        return v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        data = info.data
+        if data.get("definition_type") != "dockerfile":
+            return v
+
+        if v is None or not v.strip():
+            raise ValueError(
+                "dockerfile_template is required when definition_type is 'dockerfile'"
+            )
+
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+
+        return v
+
+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str) -> str:
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
+    @field_validator("default_port")
+    @classmethod
+    def validate_default_port(cls, v: int, info) -> int:
+        data = info.data
+        requires_port = data.get("requires_port", True)
+        if not requires_port:
+            return v
+        if v <= 0 or v > 65535:
+            raise ValueError("Port must be between 1 and 65535")
+        return v
+
+    @field_validator("required_variables")
+    @classmethod
+    def validate_required_variables(cls, v: list[str], info) -> list[str]:
+        if not v:
+            return v
+
+        data = info.data
+        if data.get("definition_type") != "compose":
+            return v
+
+        template = data.get("compose_template")
+        if not template:
+            return v
+
+        validate_required_variables(template, v)
+        return v
+
+    @model_validator(mode="after")
+    def validate_templates(self) -> "ToolTypeCreate":
+        if self.definition_type == "manifest":
+            if self.manifest_id is None:
+                raise ValueError(
+                    "manifest_id is required when definition_type is 'manifest'"
+                )
+            return self
+
+        if self.definition_type == "dockerfile" and (
+            self.dockerfile_template is None or not self.dockerfile_template.strip()
+        ):
+            raise ValueError(
+                "dockerfile_template is required when definition_type is 'dockerfile'"
+            )
+        if self.definition_type == "compose" and (
+            self.compose_template is None or not self.compose_template.strip()
+        ):
+            raise ValueError(
+                "compose_template is required when definition_type is 'compose'"
+            )
+
+        if (
+            self.requires_port
+            and self.definition_type == "compose"
+            and self.compose_template
+        ):
+            try:
+                parsed = validate_compose_yaml(self.compose_template)
+            except ValueError:
+                return self
+
+            if not check_port_exposed(parsed, self.default_port):
+                raise ValueError(
+                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
+                )
+
+        return self
+
+
+class ToolTypeUpdate(BaseModel):
+    display_name: str | None = None
+    description: str | None = None
+    default_port: int | None = None
+    definition_type: str | None = None
+    manifest_id: uuid.UUID | None = None
+    compose_template: str | None = None
+    dockerfile_template: str | None = None
+    build_context: dict | None = None
+    readiness_probe: dict | None = None
+    startup_command: str | None = None
+    required_variables: list[str] | None = None
+    category: str | None = None
+    interface_type: str | None = None
+    requires_port: bool | None = None
+
+    @field_validator("definition_type")
+    @classmethod
+    def validate_definition_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("compose", "dockerfile", "manifest"):
+            raise ValueError(
+                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
+            )
+        return v
+
+    @field_validator("interface_type")
+    @classmethod
+    def validate_interface_type(cls, v: str | None) -> str | None:
+        if v is None:
+            return v
+        if v not in ("web", "terminal"):
+            raise ValueError("interface_type must be 'web' or 'terminal'")
+        return v
+
+    @field_validator("compose_template")
+    @classmethod
+    def validate_compose_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        validate_compose_yaml(v)
+        return v
+
+    @field_validator("dockerfile_template")
+    @classmethod
+    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
+        if v is None:
+            return v
+        if not v.strip().startswith("FROM"):
+            raise ValueError("Dockerfile must start with a FROM instruction")
+        return v
+
+
+class ToolTypeResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    name: str
+    display_name: str
+    description: str | None
+    category: str
+    interface_type: str
+    requires_port: bool
+    default_port: int
+    definition_type: str
+    manifest_id: uuid.UUID | None
+    compose_template: str | None
+    dockerfile_template: str | None
+    build_context: dict | None
+    readiness_probe: dict | None
+    startup_command: str | None
+    required_variables: list[str]
+    created_by_id: uuid.UUID | None
+    created_at: datetime
+    updated_at: datetime
+
+
+class ToolTypeValidateRequest(BaseModel):
+    definition_type: str
+    compose_template: str | None = None
+    dockerfile_template: str | None = None

apps/api/src/schemas/user/__init__.py

@@ -0,0 +1,11 @@
+"""User schemas module."""
+
+from src.schemas.user.user import UserProfileResponse, UserProfileUpdate
+from src.schemas.user.user_config import UserConfigResponse, UserConfigUpdate
+
+__all__ = [
+    "UserConfigResponse",
+    "UserConfigUpdate",
+    "UserProfileResponse",
+    "UserProfileUpdate",
+]

apps/api/src/schemas/user/user.py

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

apps/api/src/schemas/user/user_config.py

@@ -0,0 +1,25 @@
+"""User config response schemas."""
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserConfigResponse(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    default_editor: str | None = None
+    theme: str = "system"
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None
+    notification_mute_categories: list[str] | None = None
+    notification_toast_level: str | None = None
+
+
+class UserConfigUpdate(BaseModel):
+    default_editor: str | None = None
+    theme: str | None = None
+    git_user_name: str | None = None
+    git_user_email: str | None = None
+    last_session_id: str | None = None
+    notification_mute_categories: list[str] | None = None
+    notification_toast_level: str | None = None

apps/api/src/seeds/__init__.py

@@ -0,0 +1 @@
+"""Database seeding utilities."""

apps/api/src/seeds/builtin_tool_types.py

@@ -0,0 +1,168 @@
+"""Seed built-in tool types into the database."""
+
+import logging
+
+from sqlalchemy import select, text
+
+from src.database import SessionLocal
+from src.models import ToolType
+
+logger = logging.getLogger(__name__)
+
+
+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
+
+
+async def seed_builtin_tool_types():
+    """Create or update built-in tool types in the database.
+
+    Built-in tool types have no creator (created_by_id=None) and provide
+    out-of-the-box tools for users without requiring manual tool creation.
+    """
+    async with SessionLocal() as session:
+        # Check if tool_types table exists before attempting to seed
+        if not await _table_exists(session, "tool_types"):
+            logger.warning(
+                "tool_types table does not exist. Skipping seeding. "
+                "Migrations may not have run yet."
+            )
+            return
+
+        builtin_types = [
+            {
+                "name": "code-server",
+                "display_name": "VS Code Server",
+                "description": "VS Code running in the browser via code-server",
+                "category": "editor",
+                "interface_type": "web",
+                "compose_template": """version: "3.8"
+services:
+  code-server:
+    image: lscr.io/linuxserver/code-server:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - PUID=1000
+      - PGID=1000
+      - TZ=Europe/London
+    volumes:
+      - {{REPO_PATH}}:/config/workspace
+    ports:
+      - "8443:8443"
+    restart: unless-stopped""",
+                "default_port": 8443,
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "jupyter-notebook",
+                "display_name": "Jupyter Notebook",
+                "description": "Jupyter Lab for interactive development",
+                "category": "notebook",
+                "interface_type": "web",
+                "default_port": 8888,
+                "compose_template": """version: "3.8"
+services:
+  jupyter:
+    image: jupyter/scipy-notebook:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - JUPYTER_ENABLE_LAB=yes
+    volumes:
+      - {{REPO_PATH}}:/home/jovyan/work
+    ports:
+      - "8888:8888"
+    restart: unless-stopped""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+            {
+                "name": "opencode",
+                "display_name": "OpenCode",
+                "description": "AI coding assistant - run opencode in terminal",
+                "category": "ai-assistant",
+                "interface_type": "terminal",
+                "default_port": 3000,
+                "compose_template": """version: "3.8"
+services:
+  opencode:
+    image: node:20-slim
+    container_name: {{TOOL_NAME}}
+    working_dir: /workspace
+    environment:
+      - HOME=/tmp
+    volumes:
+      - {{REPO_PATH}}:/workspace
+      - opencode_home:/tmp
+    ports:
+      - "3000:3000"
+    command: >
+      sh -c "set -x &&
+             apt-get update && apt-get install -y git ca-certificates &&
+             echo 'Installing opencode...' &&
+             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
+             which opencode || echo 'ERROR: opencode not in PATH' &&
+             npm bin -g &&
+             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
+             echo 'export PATH=\"$(npm bin -g):\\$PATH\"' >> /root/.bashrc &&
+             echo 'cd /workspace' >> /root/.bashrc &&
+             echo 'OpenCode installation complete' &&
+             cd /workspace &&
+             exec tail -f /dev/null"
+    stdin_open: true
+    tty: true
+    restart: unless-stopped
+
+volumes:
+  opencode_home:""",
+                "required_variables": ["REPO_PATH", "TOOL_NAME"],
+            },
+        ]
+
+        for tool_data in builtin_types:
+            existing = await session.scalar(
+                select(ToolType).where(ToolType.name == tool_data["name"])
+            )
+            if not existing:
+                tool_type = ToolType(
+                    name=tool_data["name"],
+                    display_name=tool_data["display_name"],
+                    description=tool_data["description"],
+                    category=tool_data["category"],
+                    interface_type=tool_data["interface_type"],
+                    definition_type="compose",
+                    compose_template=tool_data["compose_template"],
+                    required_variables=tool_data["required_variables"],
+                    default_port=tool_data.get("default_port", 0),
+                    created_by_id=None,
+                )
+                session.add(tool_type)
+                logger.info("Created built-in tool type: %s", tool_data["name"])
+            else:
+                # Update existing built-in tool types to reflect code changes
+                existing.display_name = tool_data["display_name"]
+                existing.description = tool_data["description"]
+                existing.category = tool_data["category"]
+                existing.interface_type = tool_data["interface_type"]
+                existing.definition_type = "compose"
+                existing.compose_template = tool_data["compose_template"]
+                existing.required_variables = tool_data["required_variables"]
+                existing.default_port = tool_data.get("default_port", 0)
+                logger.info("Updated built-in tool type: %s", tool_data["name"])
+
+        await session.commit()
+        logger.info("Built-in tool types seeded successfully.")

apps/api/src/services/build/docker_build.py

@@ -6,7 +6,9 @@ import subprocess
 logger = logging.getLogger(__name__)
 
 
-def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dict | None = None) -> tuple[int, str, str]:
+def build_image(
+    instance_dir: str, dockerfile: str, tag: str, build_context: dict | None = None
+) -> tuple[int, str, str]:
     """Build a Docker image from a Dockerfile.
 
     Args:
@@ -20,10 +22,16 @@ def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dic
     """
     from pathlib import Path
 
+    # Defensive: normalise any CRLF that may have crept in from manifest DB
+    # strings — Docker's legacy builder treats \r as a character after the
+    # backslash, breaking RUN continuations and producing
+    # "unknown instruction" errors.
+    dockerfile = dockerfile.replace("\r\n", "\n").replace("\r", "\n")
+
     # Write Dockerfile
     dockerfile_path = Path(instance_dir) / "Dockerfile"
-    dockerfile_path.write_text(dockerfile)
-    logger.debug("Wrote Dockerfile to %s", dockerfile_path)
+    dockerfile_path.write_text(dockerfile, newline="\n")
+    logger.debug("Wrote Dockerfile to %s (%d bytes)", dockerfile_path, len(dockerfile))
 
     # Write build context files
     if build_context:
@@ -33,19 +41,27 @@ def build_image(instance_dir: str, dockerfile: str, tag: str, build_context: dic
             try:
                 full_path.resolve().relative_to(Path(instance_dir).resolve())
             except ValueError:
-                logger.error("Build context file path escapes instance directory: %s", file_path)
-                raise ValueError(f"Build context file path '{file_path}' escapes instance directory")
-            
+                logger.error(
+                    "Build context file path escapes instance directory: %s", file_path
+                )
+                raise ValueError(
+                    f"Build context file path '{file_path}' escapes instance directory"
+                )
+
             full_path.parent.mkdir(parents=True, exist_ok=True)
-            full_path.write_text(content)
+            normalized = content.replace("\r\n", "\n").replace("\r", "\n")
+            full_path.write_text(normalized, newline="\n")
             logger.debug("Wrote build context file: %s", full_path)
 
     # Build image
     logger.debug("Building Docker image with tag: %s", tag)
     cmd = [
-        "docker", "build",
-        "-t", tag,
-        "-f", str(dockerfile_path),
+        "docker",
+        "build",
+        "-t",
+        tag,
+        "-f",
+        str(dockerfile_path),
         instance_dir,
     ]