merge: fix ToolDefinitionManifest runtime import in ToolType

Move the ToolDefinitionManifest import out of TYPE_CHECKING so SQLAlchemy
can resolve the string-annotated relationship when configuring the ToolType
mapper during startup.

Quality gates: py_compile and ruff passed.

.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

@@ -48,6 +48,8 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
-/.stoneforge/.worktrees/
-# Local Pi runtime state
+
+# Local runtime state
 .atl/
+.pi/
+swap-pane

.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.
 
@@ -85,6 +90,13 @@ Before completion, report:
 
 Do not claim completion without verification evidence.
 
+## Git branch policy
+
+- **Default working branch:** `dev` — all commits and pushes target `dev` unless the user explicitly requests otherwise.
+- `main` is the stable/production branch; merge to `main` only when explicitly instructed.
+- After committing, push to `origin/dev`.
+- If `dev` does not exist locally, create it from `main` or fetch it from origin.
+
 ## Git workflow
 
 ### Branching strategy

CHANGELOG.md

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

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

@@ -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

@@ -232,14 +232,6 @@ def upgrade() -> None:
                             "writable": True,
                             "owner": "user",
                         },
-                        {
-                            "name": "ssh_keys",
-                            "target": "/home/user/.ssh",
-                            "source_type": "ssh_key",
-                            "mode": "0700",
-                            "file_mode": "0600",
-                            "readonly": True,
-                        },
                         {
                             "name": "pi_state",
                             "target": "/tmp/.pi/agents",

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

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/config_profiles.py

@@ -3,721 +3,297 @@
 import logging
 import uuid
 
-from fastapi import APIRouter, Depends, HTTPException, Query, status
-from pydantic import BaseModel, Field, field_validator
+from fastapi import APIRouter, Depends, HTTPException, status
 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.project import Project
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
 from src.models.tool_type import ToolType
-from src.services.config_profile_resolver import (
-    ConfigProfileCycleError,
-    check_include_cycle,
-    resolve_profile,
-    resolved_profile_to_dict,
+from src.models.user_config import UserConfig
+from src.schemas.config_profile import (
+    ConfigIncludeCreate,
+    ConfigIncludeUpdate,
+    ConfigMountCreate,
+    ConfigMountUpdate,
+    ConfigProfileCreate,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+)
+from src.services.config_profiles import (
+    check_duplicate_include,
+    check_duplicate_mount_path,
+    check_duplicate_name,
+    get_default_profile_for_tool_type,
+    get_default_profiles,
+    get_owned_profile,
+    include_to_dict,
+    list_includes_for_profile,
+    list_mounts_for_profile,
+    mount_to_dict,
+    profile_to_dict,
+    set_default_profiles,
+    validate_includes_no_cycle,
 )
 
 logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
 
-MAX_PROFILE_SIZE_MB = 10
-MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
 
 
-def _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
-    for key, value in data.get("env_vars", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for key, value in data.get("runtime_hints", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for mount in data.get("mounts", []):
-        total += len(str(mount.get("target", "")).encode("utf-8"))
-        total += len(str(mount.get("mode", "")).encode("utf-8"))
-        for path, content in mount.get("files", {}).items():
-            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    for path, content in data.get("files", {}).items():
-        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    return total
-
-
-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:
-    """Fetch a profile with includes eagerly loaded."""
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile_id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    return result.scalar_one_or_none()
-
-
-async def _check_access(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    project_id: uuid.UUID | None = None,
-    tool_type_id: uuid.UUID | None = None,
-) -> None:
-    """Verify user has access to referenced project and tool type."""
-    if project_id is not None:
-        project = await session.get(Project, project_id)
-        if project is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project not found")
-        # Add ownership check if needed; for now just verify existence
-    if tool_type_id is not None:
-        tool_type = await session.get(ToolType, tool_type_id)
+@router.get("")
+async def list_config_profiles(
+    tool_type_id: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    query = select(ConfigProfile).where(ConfigProfile.user_id == user_id)
+    if tool_type_id:
+        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")
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    result = await session.execute(query.order_by(ConfigProfile.name))
+    return {"profiles": [profile_to_dict(p) for p in result.scalars().all()]}
 
 
-async def _validate_git_mounts(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    git_mounts: list[dict],
-    project_id: uuid.UUID | None = None,
-) -> None:
-    """Validate git mount URLs.
-    
-    Simply checks that remote_url looks like a valid git URL.
-    Actual clone validation happens at instance startup time.
-    """
-    for mount in git_mounts:
-        remote_url = mount.get("remote_url")
-        if not remote_url:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Git mount missing remote_url",
-            )
-        
-        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid git URL: {remote_url}",
-            )
+@router.post("", status_code=status.HTTP_201_CREATED)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await check_duplicate_name(session, user_id, data.name)
+    profile = ConfigProfile(user_id=user_id, name=data.name, description=data.description)
+    session.add(profile)
+    await session.commit()
+    await session.refresh(profile)
+    return profile_to_dict(profile)
 
 
-def _profile_to_response(profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None) -> dict:
+@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:
+    return await get_default_profiles(session, user_id)
+
+
+@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:
+    return await set_default_profiles(session, user_id, data.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:
+    return await get_default_profile_for_tool_type(session, user_id, tool_type_id)
+
+
+@router.get("/{profile_id}")
+async def get_config_profile(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await session.get(
+        ConfigProfile,
+        profile_id,
+        options=[selectinload(ConfigProfile.includes), selectinload(ConfigProfile.mounts)],
+    )
+    if profile is None or profile.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
+    includes_data = []
+    for inc in profile.includes:
+        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
+        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
     return {
-        "id": str(profile.id),
-        "user_id": str(profile.user_id),
-        "name": profile.name,
-        "description": profile.description,
-        "project_id": str(profile.project_id) if profile.project_id else None,
-        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
-        "env_vars": profile.env_vars or {},
-        "runtime_hints": profile.runtime_hints or {},
-        "mounts": profile.mounts or [],
-        "git_mounts": profile.git_mounts or [],
-        "files": profile.files or {},
-        "is_default": profile.is_default,
-        "includes": [
-            {
-                "id": str(inc.id),
-                "included_profile_id": str(inc.included_profile_id),
-                "order_index": inc.order_index,
-            }
-            for inc in (includes or profile.includes)
-        ],
-        "created_at": profile.created_at.isoformat() if profile.created_at else None,
-        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
+        **profile_to_dict(profile),
+        "includes": includes_data,
+        "mounts": [mount_to_dict(m) for m in profile.mounts],
     }
 
 
-@router.get("", response_model=list[ConfigProfileResponse])
-async def list_config_profiles(
-    project_id: str | None = Query(None, description="Filter by project compatibility"),
-    tool_type_id: str | None = Query(None, description="Filter by tool type compatibility"),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """List config profiles, optionally filtered by compatibility."""
-    user_uuid = current_user_id
-    query = select(ConfigProfile).where(ConfigProfile.user_id == user_uuid).options(selectinload(ConfigProfile.includes))
-
-    if project_id or tool_type_id:
-        # Compatibility filter: include portable profiles and matching scoped profiles
-        project_uuid = uuid.UUID(project_id) if project_id else None
-        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
-
-        from sqlalchemy import or_
-
-        conditions: list = []
-        # Portable profiles (no project, no tool)
-        conditions.append(
-            (ConfigProfile.project_id.is_(None)) & (ConfigProfile.tool_type_id.is_(None))
-        )
-        if project_uuid:
-            # Profiles matching this project (with or without tool)
-            conditions.append(ConfigProfile.project_id == project_uuid)
-        if tool_uuid:
-            # Profiles matching this tool (with or without project)
-            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
-        if project_uuid and tool_uuid:
-            # Exact match
-            conditions.append(
-                (ConfigProfile.project_id == project_uuid) & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-
-        query = query.where(or_(*conditions))
-
-    result = await session.execute(query)
-    profiles = result.scalars().all()
-    return [_profile_to_response(p) for p in profiles]
-
-
-@router.post("", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED)
-async def create_config_profile(
-    data: ConfigProfileCreate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Create a new config profile."""
-    user_uuid = current_user_id
-
-    # Check for duplicate name
-    existing = await session.execute(
-        select(ConfigProfile).where(
-            ConfigProfile.user_id == user_uuid,
-            ConfigProfile.name == data.name,
-        ).options(selectinload(ConfigProfile.includes))
-    )
-    if existing.scalar_one_or_none() is not None:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Profile with name '{data.name}' already exists",
-        )
-
-    # Validate references
-    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
-    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
-    await _check_access(session, user_uuid, project_uuid, tool_uuid)
-    
-    # Validate git mounts reference existing repositories
-    if data.git_mounts:
-        git_mounts_data = [m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts]
-        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
-
-    # Check size
-    size = _calculate_profile_size(data.model_dump())
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    profile = ConfigProfile(
-        user_id=user_uuid,
-        name=data.name,
-        description=data.description,
-        project_id=project_uuid,
-        tool_type_id=tool_uuid,
-        env_vars=data.env_vars,
-        runtime_hints=data.runtime_hints,
-        mounts=[m.model_dump() for m in data.mounts],
-        git_mounts=[m.model_dump() for m in data.git_mounts],
-        files=data.files,
-        is_default=data.is_default,
-    )
-    session.add(profile)
-    await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
-    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
-    return _profile_to_response(profile)
-
-
-@router.get("/{profile_id}", response_model=ConfigProfileResponse)
-async def get_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Get a config profile by ID."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-    return _profile_to_response(profile)
-
-
-@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+@router.put("/{profile_id}")
 async def update_config_profile(
-    profile_id: str,
+    profile_id: uuid.UUID,
     data: ConfigProfileUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-):
-    """Update a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    update_data = data.model_dump(exclude_unset=True)
-
-    # Handle name uniqueness
-    if "name" in update_data:
-        existing = await session.execute(
-            select(ConfigProfile).where(
-                ConfigProfile.user_id == profile.user_id,
-                ConfigProfile.name == update_data["name"],
-                ConfigProfile.id != profile.id,
-            )
-        )
-        if existing.scalar_one_or_none() is not None:
-            raise HTTPException(
-                status_code=status.HTTP_409_CONFLICT,
-                detail=f"Profile with name '{update_data['name']}' already exists",
-            )
-
-    # Validate references
-    project_uuid = (
-        uuid.UUID(update_data["project_id"])
-        if "project_id" in update_data and update_data["project_id"]
-        else (profile.project_id if "project_id" not in update_data else None)
-    )
-    tool_uuid = (
-        uuid.UUID(update_data["tool_type_id"])
-        if "tool_type_id" in update_data and update_data["tool_type_id"]
-        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
-    )
-    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
-    
-    # Validate git mounts reference existing repositories
-    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
-        git_mounts_data = [
-            m.model_dump() if hasattr(m, "model_dump") else m 
-            for m in update_data["git_mounts"]
-        ]
-        await _validate_git_mounts(session, profile.user_id, git_mounts_data, project_uuid)
-
-    # Check size
-    current_data = _profile_to_response(profile)
-    merged = {**current_data, **update_data}
-    size = _calculate_profile_size(merged)
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    # Apply updates
-    for field_name, value in update_data.items():
-        if field_name in ("project_id", "tool_type_id"):
-            value = uuid.UUID(value) if value else None
-        elif field_name == "mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        elif field_name == "git_mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        setattr(profile, field_name, value)
-
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    if data.name is not None:
+        await check_duplicate_name(session, user_id, data.name, exclude_id=profile_id)
+        profile.name = data.name
+    if data.description is not None:
+        profile.description = data.description
     await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
-    logger.debug("Updated config profile %s", profile.id)
-    return _profile_to_response(profile)
+    await session.refresh(profile)
+    return profile_to_dict(profile)
 
 
 @router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
 async def delete_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-):
-    """Delete a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
+) -> None:
+    profile = await get_owned_profile(profile_id, user_id, session)
     await session.delete(profile)
     await session.commit()
 
-    logger.debug("Deleted config profile %s", profile_id)
-    return None
 
 
-@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
-async def update_profile_includes(
-    profile_id: str,
-    data: ConfigProfileIncludeUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
+@router.get("/{profile_id}/includes")
+async def list_profile_includes(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-):
-    """Update the ordered includes for a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    return await list_includes_for_profile(session, profile_id)
 
-    # Validate all included profiles exist and belong to the user
-    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
-    for inc_uuid in included_uuids:
-        inc_profile = await session.get(ConfigProfile, inc_uuid)
-        if inc_profile is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Included profile not found: {inc_uuid}",
-            )
-        if inc_profile.user_id != current_user_id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=f"Not authorized to include profile: {inc_uuid}",
-            )
-        if inc_uuid == profile.id:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Profile cannot include itself",
-            )
 
-    # Check for cycles
-    cycle = await check_include_cycle(session, profile.id, None)
-    if cycle is None and included_uuids:
-        # Check each new include would not create a cycle
-        for inc_uuid in included_uuids:
-            cycle = await check_include_cycle(session, profile.id, inc_uuid)
-            if cycle is not None:
-                break
-
-    if cycle is not None:
-        cycle_str = " -> ".join(str(c) for c in cycle)
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Include cycle detected: {cycle_str}",
-        )
-
-    # Remove existing includes
-    result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
+@router.post("/{profile_id}/includes", status_code=status.HTTP_201_CREATED)
+async def add_profile_include(
+    profile_id: uuid.UUID,
+    data: ConfigIncludeCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    included_profile_id = uuid.UUID(data.included_profile_id)
+    if included_profile_id == profile_id:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="a profile cannot include itself")
+    included_profile = await session.get(ConfigProfile, included_profile_id)
+    if included_profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="included profile not found")
+    if included_profile.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="included profile does not belong to user")
+    await check_duplicate_include(session, profile_id, included_profile_id)
+    await validate_includes_no_cycle(session, profile_id, included_profile_id)
+    include = ConfigInclude(
+        profile_id=profile_id,
+        included_profile_id=included_profile_id,
+        order_index=data.order_index,
     )
-    for existing in result.scalars().all():
-        await session.delete(existing)
-    await session.flush()
+    session.add(include)
+    await session.commit()
+    await session.refresh(include)
+    return include_to_dict(include, included_profile.name)
 
-    # Add new includes
-    for order_index, inc_uuid in enumerate(included_uuids):
-        include = ConfigProfileInclude(
-            profile_id=profile.id,
-            included_profile_id=inc_uuid,
-            order_index=order_index,
-        )
-        session.add(include)
-    await session.flush()
 
+@router.put("/{profile_id}/includes/{include_id}")
+async def update_profile_include(
+    profile_id: uuid.UUID,
+    include_id: uuid.UUID,
+    data: ConfigIncludeUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    include = await session.get(ConfigInclude, include_id)
+    if include is None or include.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
+    include.order_index = data.order_index
+    await session.commit()
+    await session.refresh(include)
+    included_profile = await session.get(ConfigProfile, include.included_profile_id)
+    return include_to_dict(include, included_profile.name if included_profile else None)
+
+
+@router.delete("/{profile_id}/includes/{include_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def remove_profile_include(
+    profile_id: uuid.UUID,
+    include_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    await get_owned_profile(profile_id, user_id, session)
+    include = await session.get(ConfigInclude, include_id)
+    if include is None or include.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
+    await session.delete(include)
     await session.commit()
 
-    # Re-fetch profile (includes loaded separately due to SQLite async issue)
-    result = await session.execute(
-        select(ConfigProfile).where(ConfigProfile.id == profile.id)
-    )
-    profile = result.scalar_one()
-
-    inc_result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
-    )
-    direct_includes = inc_result.scalars().all()
-
-    logger.debug("Updated includes for config profile %s", profile.id)
-    return _profile_to_response(profile, list(direct_includes))
 
 
-@router.get("/{profile_id}/preview")
-async def preview_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
+@router.get("/{profile_id}/mounts")
+async def list_profile_mounts(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-):
-    """Preview the resolved output of a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    try:
-        resolved = await resolve_profile(session, profile.id)
-    except ConfigProfileCycleError as exc:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=str(exc),
-        )
-
-    return resolved_profile_to_dict(resolved)
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    return await list_mounts_for_profile(session, profile_id)
 
 
-@router.get("/defaults/resolve")
-async def resolve_default_profile(
-    project_id: str = Query(..., description="Project ID"),
-    tool_type_id: str = Query(..., description="Tool type ID"),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
+@router.post("/{profile_id}/mounts", status_code=status.HTTP_201_CREATED)
+async def add_profile_mount(
+    profile_id: uuid.UUID,
+    data: ConfigMountCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-):
-    """Resolve the default config profile for a project/tool combination.
-
-    Selects by specificity:
-    1. project+tool explicit default
-    2. project explicit default
-    3. tool explicit default
-    4. global/user explicit default
-    5. first created compatible profile
-    6. none (returns null)
-    """
-    user_uuid = current_user_id
-    project_uuid = uuid.UUID(project_id)
-    tool_uuid = uuid.UUID(tool_type_id)
-
-    # Fetch all compatible profiles ordered by created_at
-    query = (
-        select(ConfigProfile)
-        .where(ConfigProfile.user_id == user_uuid)
-        .where(
-            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
-            | (ConfigProfile.project_id == project_uuid)
-            | (ConfigProfile.tool_type_id == tool_uuid)
-            | (
-                (ConfigProfile.project_id == project_uuid)
-                & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-        )
-        .order_by(ConfigProfile.created_at)
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    await check_duplicate_mount_path(session, profile_id, data.target_path)
+    mount = ConfigMount(
+        profile_id=profile_id,
+        target_path=data.target_path,
+        mode=data.mode,
+        files=data.files,
+        order_index=data.order_index,
     )
-    result = await session.execute(query)
-    profiles = result.scalars().all()
+    session.add(mount)
+    await session.commit()
+    await session.refresh(mount)
+    return mount_to_dict(mount)
 
-    if not profiles:
-        return {"profile_id": None, "profile_name": None}
 
-    # Check explicit defaults by specificity
-    explicit_defaults = [p for p in profiles if p.is_default]
+@router.put("/{profile_id}/mounts/{mount_id}")
+async def update_profile_mount(
+    profile_id: uuid.UUID,
+    mount_id: uuid.UUID,
+    data: ConfigMountUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    mount = await session.get(ConfigMount, mount_id)
+    if mount is None or mount.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
+    if data.target_path is not None:
+        await check_duplicate_mount_path(session, profile_id, data.target_path, exclude_id=mount_id)
+        mount.target_path = data.target_path
+    if data.files is not None:
+        mount.files = data.files
+    if data.order_index is not None:
+        mount.order_index = data.order_index
+    await session.commit()
+    await session.refresh(mount)
+    return mount_to_dict(mount)
 
-    # Most specific: project+tool
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
 
-    # Next: project only
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: tool only
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: global/user (no project, no tool)
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Fall back to first created compatible profile
-    first = profiles[0]
-    return {"profile_id": str(first.id), "profile_name": first.name}
+@router.delete("/{profile_id}/mounts/{mount_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def remove_profile_mount(
+    profile_id: uuid.UUID,
+    mount_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    await get_owned_profile(profile_id, user_id, session)
+    mount = await session.get(ConfigMount, mount_id)
+    if mount is None or mount.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
+    await session.delete(mount)
+    await session.commit()

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

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

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

apps/api/src/api/projects.py

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

apps/api/src/api/ssh_keys.py

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

apps/api/src/api/terminal.py

@@ -4,25 +4,17 @@ import asyncio
 import logging
 import uuid
 
-from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
+from fastapi import APIRouter, Depends, WebSocket
 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",
 )
@@ -34,7 +26,11 @@ async def terminal_websocket(
     """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.
+    Supports:
+    - Auto-reconnection (client reconnects, server spawns new session)
+    - Heartbeat ping/pong
+    - Binary and text input frames
+    - Graceful session end notifications
 
     Args:
         websocket: The WebSocket connection.
@@ -43,27 +39,27 @@ async def terminal_websocket(
 
     Returns:
         None. Communicates via WebSocket messages.
+
     """
-    logger.debug("Terminal WebSocket connection attempt for instance %s", instance_id)
+    logger.info("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)
+        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)
@@ -71,229 +67,66 @@ async def terminal_websocket(
         return
 
     if instance.owner_id != user_id:
-        logger.warning("Forbidden terminal access for instance %s by user %s", instance_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)
+        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
+    logger.info(
+        "Creating terminal session for instance %s (container_id=%s)",
+        instance_id,
+        instance.container_id,
+    )
     try:
-        session = await terminal_manager.get_or_create_session(
+        session = await terminal_manager.create_session(
             instance_uuid,
             instance.container_id,
-            startup_command=startup_command,
+            websocket,
+        )
+        logger.info(
+            "Terminal session created successfully for instance %s",
+            instance_id,
         )
-        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)
+        # Monitor session health and echo state
+        while session.is_alive() and not session.closed:
+            # Check echo state periodically
+            new_echo_state = await session.check_echo_state()
+            if new_echo_state is not None:
+                await websocket.send_json(
+                    {"type": "set_echo_state", "enabled": new_echo_state},
+                )
+            await asyncio.sleep(1.0)
 
-        # 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)
+        # Session ended — determine reason and notify client
+        exit_reason = session.get_exit_reason() or "process_exit"
+        await websocket.send_json({"type": "session_ended", "reason": exit_reason})
+        await websocket.close(code=1000, reason=f"Session ended: {exit_reason}")
 
-        # 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(
+        logger.exception(
+            "Terminal session error for instance %s",
             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}"
         )
+        await websocket.close(code=4000, reason="Terminal session error")
+    finally:
+        pass
 
 
 async def _get_user_from_websocket(
@@ -308,6 +141,7 @@ async def _get_user_from_websocket(
 
     Returns:
         The user's UUID if authenticated, None otherwise.
+
     """
     from src.auth.session import decode_session_cookie
     from src.config import Settings

apps/api/src/api/tool_configs.py

@@ -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/tool_types.py

@@ -1,19 +1,19 @@
 import uuid
-from datetime import datetime
 
+import yaml
 from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.api.tool_types_validation import (
-    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.auth.dependencies import get_current_user, get_db_session
 from src.models.tool_type import ToolType
 from src.models.user import User
+from src.schemas.tool_type import (
+    ToolTypeCreate,
+    ToolTypeResponse,
+    ToolTypeUpdate,
+    ToolTypeValidateRequest,
+)
 
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
 
@@ -29,203 +29,6 @@ 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,
@@ -235,7 +38,7 @@ class ToolTypeResponse(BaseModel):
 )
 async def create_tool_type(
     data: ToolTypeCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Create a new tool type.
@@ -248,14 +51,16 @@ async def create_tool_type(
     Returns:
         The newly created tool type.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
-    
+
     # Check for duplicate name
     existing = await session.scalar(select(ToolType).where(ToolType.name == data.name))
     if existing:
-        raise HTTPException(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,
@@ -266,11 +71,9 @@ async def create_tool_type(
         dockerfile_template=data.dockerfile_template,
         build_context=data.build_context,
         readiness_probe=data.readiness_probe,
-        startup_command=data.startup_command,
         required_variables=data.required_variables,
         category=data.category,
-        interface_type=data.interface_type,
-        requires_port=data.requires_port,
+        interfaces=data.interfaces,
         created_by_id=user.id,
     )
     session.add(tool_type)
@@ -286,7 +89,7 @@ async def create_tool_type(
     description="List all available tool types including built-in and custom ones.",
 )
 async def list_tool_types(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> list[ToolType]:
     """List all tool types.
@@ -298,7 +101,6 @@ async def list_tool_types(
     Returns:
         List of all tool types ordered by name.
     """
-    await _get_user(session, user_id)
     result = await session.execute(select(ToolType).order_by(ToolType.name))
     return list(result.scalars().all())
 
@@ -311,7 +113,7 @@ async def list_tool_types(
 )
 async def get_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Get a specific tool type by ID.
@@ -324,10 +126,11 @@ async def get_tool_type(
     Returns:
         The requested tool type.
     """
-    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(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
 
 
@@ -340,7 +143,7 @@ async def get_tool_type(
 async def update_tool_type(
     tool_type_id: uuid.UUID,
     data: ToolTypeUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
     """Update a tool type.
@@ -354,71 +157,102 @@ async def update_tool_type(
     Returns:
         The updated tool type.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
-    
+
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    # Built-in tool types can now be modified
-    
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+
+    if tool_type.is_builtin:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN,
+            detail="cannot modify built-in tool types",
+        )
+
     update_data = data.model_dump(exclude_unset=True)
-    
+
     # Validate port if being updated
-    requires_port = update_data.get("requires_port", tool_type.requires_port)
-    if "default_port" in update_data and requires_port:
+    if "default_port" in update_data:
         new_port = update_data["default_port"]
         if new_port <= 0 or new_port > 65535:
             raise HTTPException(
                 status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Port must be between 1 and 65535"
+                detail="Port must be between 1 and 65535",
             )
-        
+
         # Only validate port exposure for compose definitions
         definition_type = update_data.get("definition_type", tool_type.definition_type)
         if definition_type == "compose":
             template = update_data.get("compose_template", tool_type.compose_template)
             if template:
                 try:
-                    parsed = validate_compose_yaml(template)
-                    if not check_port_exposed(parsed, new_port):
+                    parsed = yaml.safe_load(template)
+                except yaml.YAMLError:
+                    parsed = None
+
+                if parsed and isinstance(parsed, dict) and "services" in parsed:
+                    port_str = str(new_port)
+                    port_exposed = False
+                    for service_config in parsed["services"].values():
+                        if (
+                            isinstance(service_config, dict)
+                            and "ports" in service_config
+                        ):
+                            for port_mapping in service_config["ports"]:
+                                if (
+                                    isinstance(port_mapping, str)
+                                    and port_str in port_mapping
+                                ):
+                                    port_exposed = True
+                                    break
+                                elif (
+                                    isinstance(port_mapping, int)
+                                    and port_mapping == new_port
+                                ):
+                                    port_exposed = True
+                                    break
+                        if port_exposed:
+                            break
+
+                    if not port_exposed:
                         raise HTTPException(
                             status_code=status.HTTP_400_BAD_REQUEST,
-                            detail=f"Port {new_port} is not exposed in the compose template"
+                            detail=f"Port {new_port} is not exposed in the compose template",
                         )
-                except ValueError as e:
-                    raise HTTPException(
-                        status_code=status.HTTP_400_BAD_REQUEST,
-                        detail=str(e)
-                    )
 
     # Validate required variables for compose definitions
     definition_type = update_data.get("definition_type", tool_type.definition_type)
     if definition_type == "compose":
         if "required_variables" in update_data and "compose_template" in update_data:
-            validate_required_variables(
-                update_data["compose_template"], update_data["required_variables"]
-            )
+            template = update_data["compose_template"]
+            for var in update_data["required_variables"]:
+                placeholder = f"{{{{{var}}}}}"
+                if placeholder not in template:
+                    raise HTTPException(
+                        status_code=status.HTTP_400_BAD_REQUEST,
+                        detail=f"Required variable '{var}' not found in compose template",
+                    )
         elif "required_variables" in update_data:
             template = tool_type.compose_template
             if template:
-                validate_required_variables(template, update_data["required_variables"])
-    
+                for var in update_data["required_variables"]:
+                    placeholder = f"{{{{{var}}}}}"
+                    if placeholder not in template:
+                        raise HTTPException(
+                            status_code=status.HTTP_400_BAD_REQUEST,
+                            detail=f"Required variable '{var}' not found in compose template",
+                        )
+
     for field, value in update_data.items():
         setattr(tool_type, field, value)
-    
+
     await session.commit()
     await session.refresh(tool_type)
     return tool_type
 
 
-class ToolTypeValidateRequest(BaseModel):
-    definition_type: str
-    compose_template: str | None = None
-    dockerfile_template: str | None = None
-
-
 @router.post(
     "/validate",
     summary="Validate tool type template",
@@ -426,7 +260,7 @@ class ToolTypeValidateRequest(BaseModel):
 )
 async def validate_tool_type_template(
     data: ToolTypeValidateRequest,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type template syntax.
@@ -439,7 +273,6 @@ async def validate_tool_type_template(
     Returns:
         Validation result with success status and any errors.
     """
-    await _get_user(session, user_id)
 
     errors = []
 
@@ -448,9 +281,15 @@ async def validate_tool_type_template(
             errors.append("Compose template is required")
         else:
             try:
-                validate_compose_yaml(data.compose_template)
-            except ValueError as e:
-                errors.append(str(e))
+                parsed = yaml.safe_load(data.compose_template)
+                if not isinstance(parsed, dict):
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
 
     elif data.definition_type == "dockerfile":
         if not data.dockerfile_template:
@@ -474,7 +313,7 @@ async def validate_tool_type_template(
 )
 async def validate_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict:
     """Validate a tool type's template syntax.
@@ -487,28 +326,35 @@ async def validate_tool_type(
     Returns:
         Validation result with success status and any errors.
     """
-    await _get_user(session, user_id)
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(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")
         else:
             try:
-                validate_compose_yaml(tool_type.compose_template)
-            except ValueError as e:
-                errors.append(str(e))
-    
+                parsed = yaml.safe_load(tool_type.compose_template)
+                if not isinstance(parsed, dict):
+                    errors.append("Compose template must be a YAML mapping")
+                elif "services" not in parsed:
+                    errors.append("Compose template must contain 'services' key")
+                elif not parsed["services"]:
+                    errors.append("Compose template must define at least one service")
+            except yaml.YAMLError as e:
+                errors.append(f"Invalid YAML: {e}")
+
     elif tool_type.definition_type == "dockerfile":
         if not tool_type.dockerfile_template:
             errors.append("Dockerfile template is empty")
         elif not tool_type.dockerfile_template.strip().startswith("FROM"):
             errors.append("Dockerfile must start with a FROM instruction")
-    
+
     return {
         "valid": len(errors) == 0,
         "errors": errors,
@@ -523,7 +369,7 @@ async def validate_tool_type(
 )
 async def delete_tool_type(
     tool_type_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
     """Delete a tool type.
@@ -536,14 +382,19 @@ async def delete_tool_type(
     Returns:
         None with 204 status code.
     """
-    user = await _get_user(session, user_id)
     await _require_admin(user)
-    
+
     tool_type = await session.get(ToolType, tool_type_id)
     if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    
-    # Built-in tool types can now be deleted
-    
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
+        )
+
+    if tool_type.is_builtin:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN,
+            detail="cannot delete built-in tool types",
+        )
+
     await session.delete(tool_type)
     await session.commit()

apps/api/src/api/user_config.py

@@ -1,19 +1,19 @@
 import logging
 import uuid
 
-from fastapi import APIRouter, Depends
-from pydantic import BaseModel, ConfigDict
+from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import get_current_user, get_db_session
+from src.models.user import User
 from src.models.user_config import UserConfig
-
-logger = logging.getLogger(__name__)
+from src.schemas.user_config import UserConfigResponse, UserConfigUpdate
 
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
+
 async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
     """Get or create user config record.
 
@@ -24,34 +24,16 @@ 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={})
+        config = UserConfig(user_id=user.id, config={})
         session.add(config)
         await session.commit()
         await session.refresh(config)
     return config
 
 
-class UserConfigResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    default_editor: str | None = None
-    theme: str = "system"
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-
-
-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,
@@ -59,7 +41,7 @@ class UserConfigUpdate(BaseModel):
     description="Get the current user's configuration settings.",
 )
 async def get_user_config(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Get the current user's configuration.
@@ -71,8 +53,7 @@ async def get_user_config(
     Returns:
         The user's configuration settings.
     """
-    _user = await _get_user(session, user_id)
-    config = await _get_or_create_config(session, user_id)
+    config = await _get_or_create_config(session, user.id)
     return UserConfigResponse.model_validate(config.config)
 
 
@@ -84,7 +65,7 @@ async def get_user_config(
 )
 async def update_user_config(
     data: UserConfigUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
     """Update the current user's configuration.
@@ -97,16 +78,15 @@ async def update_user_config(
     Returns:
         The updated user configuration.
     """
-    _user = await _get_user(session, user_id)
-    config = await _get_or_create_config(session, user_id)
+    config = await _get_or_create_config(session, user.id)
 
     # Merge updates
     update_data = data.model_dump(exclude_unset=True)
-    logger.debug("Updating user config for user %s: %s", user_id, update_data)
+    logger.info("Updating user config for user %s: %s", user.id, update_data)
     # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
     config.config = {**config.config, **update_data}
 
     await session.commit()
     await session.refresh(config)
-    logger.debug("Updated config: %s", config.config)
+    logger.info("Updated config: %s", config.config)
     return UserConfigResponse.model_validate(config.config)

apps/api/src/api/users.py

@@ -2,11 +2,14 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from pydantic import BaseModel, ConfigDict
+from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.auth.dependencies import get_current_user, get_db_session
+from src.models.tool_instance import ToolInstance
 from src.models.user import User
+from src.schemas.tool_instance import SessionItemResponse, SessionListResponse
+from src.schemas.user import UserProfileResponse, UserProfileUpdate
 
 router = APIRouter(prefix="/users", tags=["users"])
 
@@ -16,20 +19,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 
 
-class UserProfileResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    email: str
-    name: str
-    avatar_url: str | None
-
-
-class UserProfileUpdate(BaseModel):
-    name: str | None = None
-    email: str | None = None
-
-
 @router.get(
     "/me",
     response_model=UserProfileResponse,
@@ -37,7 +26,7 @@ class UserProfileUpdate(BaseModel):
     description="Retrieve the profile of the currently authenticated user.",
 )
 async def get_profile(
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Get the current user's profile.
@@ -49,7 +38,7 @@ async def get_profile(
     Returns:
         The user's profile information.
     """
-    return await _get_user(session, user_id)
+    return user
 
 
 @router.put(
@@ -60,7 +49,7 @@ async def get_profile(
 )
 async def update_profile(
     data: UserProfileUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Update the current user's profile.
@@ -73,16 +62,19 @@ async def update_profile(
     Returns:
         The updated user profile.
     """
-    user = await _get_user(session, user_id)
 
     if data.name is not None:
         if len(data.name.strip()) == 0:
-            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()
@@ -98,7 +90,7 @@ async def update_profile(
 )
 async def upload_avatar(
     file: UploadFile,
-    user_id: uuid.UUID = Depends(get_current_user_id),
+    user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> User:
     """Upload a profile avatar image.
@@ -111,7 +103,6 @@ async def upload_avatar(
     Returns:
         The updated user profile with new avatar URL.
     """
-    user = await _get_user(session, user_id)
 
     if file.content_type not in ALLOWED_CONTENT_TYPES:
         raise HTTPException(
@@ -146,3 +137,41 @@ async def upload_avatar(
     await session.commit()
     await session.refresh(user)
     return user
+
+
+@router.get(
+    "/me/sessions",
+    response_model=SessionListResponse,
+    summary="Get current user sessions",
+    description="Retrieve all tool instances (sessions) for the authenticated user.",
+)
+async def get_user_sessions(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> SessionListResponse:
+    """Return all tool instances for the current user with related names."""
+    result = await session.execute(
+        select(ToolInstance)
+        .where(ToolInstance.owner_id == user.id)
+        .order_by(ToolInstance.created_at.desc())
+    )
+    instances = result.scalars().all()
+
+    sessions = [
+        SessionItemResponse(
+            id=str(inst.id),
+            display_name=inst.display_name,
+            tool_type_name=inst.tool_type.display_name if inst.tool_type else "Unknown",
+            tool_icon=None,
+            tool_type_interfaces=inst.tool_type.interfaces if inst.tool_type else [],
+            repository_name=inst.repository.name if inst.repository else "Unknown",
+            repository_id=str(inst.repository_id),
+            project_name=inst.project.name if inst.project else "Unknown",
+            project_id=str(inst.project_id),
+            status=inst.status,
+            url=inst.url,
+        )
+        for inst in instances
+    ]
+
+    return SessionListResponse(sessions=sessions)

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

apps/api/src/api/workspace_git.py

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

apps/api/src/api/workspace_instances.py

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

apps/api/src/api/workspaces.py

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

apps/api/src/auth/dependencies.py

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

apps/api/src/logging_config.py

@@ -1,15 +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.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

@@ -6,7 +6,6 @@ from fastapi.exceptions import RequestValidationError
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from fastapi.staticfiles import StaticFiles
-
 from src.api.auth import router as auth_router
 from src.api.dashboard import router as dashboard_router
 from src.api.git_repositories import router as git_repositories_router
@@ -15,12 +14,8 @@ 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_definitions import router as tool_definitions_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
@@ -31,6 +26,7 @@ from src.logging_config import (
     RequestLoggingMiddleware,
     configure_logging,
 )
+from src.seeds.builtin_tool_types import seed_builtin_tool_types
 
 # Configure logging early
 log_level = os.getenv("LOG_LEVEL", "INFO").upper()
@@ -116,6 +112,8 @@ async def on_startup():
 
         sys.exit(1)
 
+    # Seed built-in data
+    await seed_builtin_tool_types()
     logger.info("Startup complete.")
 
 
@@ -128,12 +126,8 @@ app.include_router(ssh_keys_router)
 app.include_router(git_repositories_router)
 app.include_router(user_config_router)
 app.include_router(tool_types_router)
-app.include_router(tool_definitions_router)
-app.include_router(config_folders_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
-app.include_router(tool_configs_router)
-app.include_router(sessions_router)
 app.include_router(instance_proxy_router)
 app.include_router(terminal_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")

apps/api/src/models/__init__.py

@@ -1,10 +1,10 @@
 from src.models.base import Base
-from src.models.config_folder import ConfigFolder
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
 from src.models.git_repository import GitRepository
 from src.models.project import Project
 from src.models.ssh_key import SSHKey
-from src.models.tool_definition_manifest import ToolDefinitionManifest
 from src.models.tool_instance import ToolInstance
 from src.models.tool_type import ToolType
 from src.models.user import User
@@ -12,13 +12,12 @@ from src.models.user_config import UserConfig
 
 __all__ = [
     "Base",
-    "ConfigFolder",
+    "ConfigInclude",
+    "ConfigMount",
     "ConfigProfile",
-    "ConfigProfileInclude",
     "GitRepository",
     "Project",
     "SSHKey",
-    "ToolDefinitionManifest",
     "ToolInstance",
     "ToolType",
     "User",

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/config_include.py

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

apps/api/src/models/config_mount.py

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

apps/api/src/models/config_profile.py

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

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

@@ -2,7 +2,7 @@ import uuid
 from datetime import datetime
 from typing import TYPE_CHECKING
 
-from sqlalchemy import DateTime, ForeignKey, Integer, JSON, String
+from sqlalchemy import DateTime, ForeignKey, Integer, String
 from sqlalchemy import Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
@@ -33,30 +33,37 @@ 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
     )
-    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(
+    selected_profile_id: Mapped[uuid.UUID | None] = mapped_column(
         UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
     )
 
@@ -64,4 +71,4 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     repository: Mapped["GitRepository"] = relationship()
     project: Mapped["Project"] = relationship()
     owner: Mapped["User"] = relationship()
-    selected_config_profile: Mapped["ConfigProfile | None"] = relationship()
+    selected_profile: Mapped["ConfigProfile | None"] = relationship()

apps/api/src/models/tool_type.py

@@ -1,14 +1,14 @@
 import uuid
 from typing import TYPE_CHECKING
 
-from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
+from sqlalchemy import Boolean, ForeignKey, JSON, String, Text, Uuid as UUID
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
 
+from src.models.tool_definition_manifest import ToolDefinitionManifest
+
 if TYPE_CHECKING:
-    from src.models.tool_definition_manifest import ToolDefinitionManifest
     from src.models.user import User
 
 
@@ -52,3 +52,21 @@ class ToolType(UUIDPrimaryKeyMixin, TimestampMixin, Base):
         foreign_keys=[manifest_id],
     )
     created_by: Mapped["User | None"] = relationship()
+
+    @property
+    def interfaces(self) -> list[str]:
+        """Backward-compatible API view for the single interface type."""
+        return [self.interface_type]
+
+    @interfaces.setter
+    def interfaces(self, value: list[str] | str) -> None:
+        """Accept legacy interface lists and store the first interface type."""
+        if isinstance(value, str):
+            self.interface_type = value
+            return
+        self.interface_type = value[0] if value else "web"
+
+    @property
+    def is_builtin(self) -> bool:
+        """Built-in tools are seeded system tools without a creating user."""
+        return self.created_by_id is None

apps/api/src/models/user_config.py

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

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

apps/api/src/schemas/__init__.py

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

apps/api/src/schemas/config_profile.py

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

apps/api/src/schemas/git_repository.py

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

apps/api/src/schemas/health.py

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

apps/api/src/schemas/project.py

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

apps/api/src/schemas/ssh_key.py

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

apps/api/src/schemas/tool_instance.py

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

apps/api/src/schemas/tool_type.py

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

apps/api/src/schemas/user.py

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

apps/api/src/schemas/user_config.py

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

apps/api/src/seeds/builtin_tool_types.py

@@ -0,0 +1,162 @@
+import logging
+
+from sqlalchemy import select
+
+from src.database import SessionLocal
+from src.models.tool_type import ToolType
+
+logger = logging.getLogger(__name__)
+
+
+async def _table_exists(session, table_name: str) -> bool:
+    """Check if a table exists in the database."""
+    from sqlalchemy import text
+
+    try:
+        result = await session.execute(
+            text(
+                """
+                SELECT EXISTS (
+                    SELECT FROM information_schema.tables
+                    WHERE table_schema = 'public'
+                    AND table_name = :table_name
+                )
+            """
+            ),
+            {"table_name": table_name},
+        )
+        return result.scalar() or False
+    except Exception:
+        return False
+
+
+async def seed_builtin_tool_types():
+    async with SessionLocal() as session:
+        # Check if tool_types table exists before attempting to seed
+        if not await _table_exists(session, "tool_types"):
+            logger.warning(
+                "tool_types table does not exist. Skipping seeding. "
+                "Migrations may not have run yet."
+            )
+            return
+
+        builtin_types = [
+            {
+                "name": "code-server",
+                "display_name": "VS Code Server",
+                "description": "VS Code running in the browser via code-server",
+                "category": "editor",
+                "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["default_port"],
+                )
+                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["default_port"]
+                logger.info("Updated built-in tool type: %s", tool_data["name"])
+
+        await session.commit()
+        logger.info("Built-in tool types seeded successfully.")

apps/api/src/services/config_profile_resolver.py

@@ -5,6 +5,7 @@ and cycle protection.
 """
 
 import logging
+import os
 import uuid
 from dataclasses import dataclass, field
 from typing import Any
@@ -57,7 +58,9 @@ class ResolvedProfile:
     included_profiles: list[dict[str, Any]] = field(default_factory=list)
 
 
-def _detect_cycle(profile_id: uuid.UUID, visited: set[uuid.UUID], path: list[uuid.UUID]) -> bool:
+def _detect_cycle(
+    profile_id: uuid.UUID, visited: set[uuid.UUID], path: list[uuid.UUID]
+) -> bool:
     """Detect if adding profile_id to path would create a cycle.
 
     Args:
@@ -176,21 +179,59 @@ def _merge_git_mounts(
 ) -> list[dict[str, Any]]:
     """Merge git mounts from included profiles.
 
-    Later mounts override earlier ones with the same remote_url + target_path combo.
+    Entries with the same remote_url + branch have their mappings concatenated.
+    Different repos are kept as separate entries.
+    All entries are normalized to the mappings format.
     """
     result = list(base)
-    # Build lookup by (remote_url, target_path)
-    seen = {(m["remote_url"], m["target_path"]): i for i, m in enumerate(result)}
+    # Normalize existing entries to mappings format
+    for i, m in enumerate(result):
+        result[i] = _normalize_git_mount_entry(dict(m))
+
+    # Build lookup by (remote_url, branch)
+    seen = {}
+    for i, m in enumerate(result):
+        key = (m["remote_url"], m.get("branch"))
+        seen[key] = i
+
     for mount in overlay:
-        key = (mount["remote_url"], mount["target_path"])
+        mount = _normalize_git_mount_entry(dict(mount))
+        key = (mount["remote_url"], mount.get("branch"))
         if key in seen:
-            result[seen[key]] = dict(mount)
+            # Same repo+branch: concatenate mappings, dedup by (source_path, target_path)
+            existing = result[seen[key]]
+            existing_sources = {
+                (m["source_path"], m["target_path"])
+                for m in existing.get("mappings", [])
+            }
+            for mapping in mount.get("mappings", []):
+                map_key = (mapping["source_path"], mapping["target_path"])
+                if map_key not in existing_sources:
+                    existing["mappings"].append(dict(mapping))
+                    existing_sources.add(map_key)
         else:
             seen[key] = len(result)
-            result.append(dict(mount))
+            result.append(mount)
     return result
 
 
+def _normalize_git_mount_entry(entry: dict[str, Any]) -> dict[str, Any]:
+    """Normalize a git mount entry to the unified mappings format.
+
+    Converts legacy source_path + target_path into a single-entry mappings array.
+    """
+    entry = dict(entry)
+    if "mappings" not in entry or not entry.get("mappings"):
+        source = entry.get("source_path", ".")
+        target = entry.get("target_path")
+        if target is not None:
+            entry["mappings"] = [{"source_path": source, "target_path": target}]
+    # Remove legacy fields once normalized
+    entry.pop("source_path", None)
+    entry.pop("target_path", None)
+    return entry
+
+
 async def _resolve_profile_recursive(
     session: AsyncSession,
     profile_id: uuid.UUID,
@@ -214,7 +255,9 @@ async def _resolve_profile_recursive(
     """
     if _detect_cycle(profile_id, visited, path):
         cycle_path = " -> ".join(str(p) for p in path + [profile_id])
-        raise ConfigProfileCycleError(f"Cycle detected in profile includes: {cycle_path}")
+        raise ConfigProfileCycleError(
+            f"Cycle detected in profile includes: {cycle_path}"
+        )
 
     profile = await session.get(ConfigProfile, profile_id)
     if profile is None:
@@ -241,13 +284,18 @@ async def _resolve_profile_recursive(
         included = await _resolve_profile_recursive(
             session, include.included_profile_id, new_visited, new_path
         )
-        result.included_profiles.append({
-            "id": str(included.profile_id),
-            "name": included.profile_name,
-        })
+        result.included_profiles.append(
+            {
+                "id": str(included.profile_id),
+                "name": included.profile_name,
+            }
+        )
 
         result.env_vars = _merge_env_vars(
-            result.env_vars, included.env_vars, result.env_overrides, included.profile_name
+            result.env_vars,
+            included.env_vars,
+            result.env_overrides,
+            included.profile_name,
         )
         result.runtime_hints = _merge_runtime_hints(
             result.runtime_hints,
@@ -391,6 +439,7 @@ async def check_include_cycle(
 def apply_resolved_profile(
     instance_dir: str,
     resolved: ResolvedProfile,
+    home_dir: str = "/root",
 ) -> tuple[dict[str, str], dict[str, str], list[dict], dict[str, Any]]:
     """Apply a resolved profile to an instance directory.
 
@@ -420,14 +469,19 @@ def apply_resolved_profile(
         try:
             full_path.resolve().relative_to(instance_path.resolve())
         except ValueError:
-            logger.warning("Profile file path escapes instance directory: %s", file_path)
+            logger.warning(
+                "Profile file path escapes instance directory: %s", file_path
+            )
             continue
         full_path.parent.mkdir(parents=True, exist_ok=True)
         full_path.write_text(content)
 
     # Stage mount files and prepare volume mounts
     for mount in resolved.mounts.values():
-        mount_dir = instance_path / "mounts" / mount.target.lstrip("/").replace("/", "_")
+        expanded_target = expand_container_path(mount.target, home_dir)
+        mount_dir = (
+            instance_path / "mounts" / expanded_target.lstrip("/").replace("/", "_")
+        )
         mount_dir.mkdir(parents=True, exist_ok=True)
 
         for file_path, content in mount.files.items():
@@ -440,15 +494,44 @@ def apply_resolved_profile(
             full_path.parent.mkdir(parents=True, exist_ok=True)
             full_path.write_text(content)
 
-        volume_mounts.append({
-            "source": str(mount_dir),
-            "target": mount.target,
-            "type": "bind",
-        })
+            # Mount each file individually so sibling files from other mounts
+            # (e.g. git repo directories) are preserved.
+            file_target = os.path.join(expanded_target, file_path)
+            volume_mounts.append(
+                {
+                    "source": str(full_path),
+                    "target": file_target,
+                    "type": "bind",
+                }
+            )
 
     return env_vars, files, volume_mounts, resolved.runtime_hints
 
 
+def expand_container_path(path: str, home_dir: str) -> str:
+    """Expand ~ and $HOME in a container path to the actual home directory.
+
+    Only expands at the start of the path (e.g., ~/foo, $HOME/foo, $HOME).
+    Leaves mid-string occurrences unchanged.
+
+    Args:
+        path: Container path that may contain ~ or $HOME.
+        home_dir: The container's home directory (e.g., /home/user or /root).
+
+    Returns:
+        Path with ~ and $HOME expanded.
+    """
+    if path.startswith("~/"):
+        return os.path.join(home_dir, path[2:])
+    if path == "~":
+        return home_dir
+    if path.startswith("$HOME/"):
+        return home_dir + "/" + path[6:]
+    if path == "$HOME":
+        return home_dir
+    return path
+
+
 def resolved_profile_to_dict(resolved: ResolvedProfile) -> dict[str, Any]:
     """Convert a ResolvedProfile to a plain dict for serialization.
 

apps/api/src/services/config_profiles.py

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

apps/api/src/services/correlation.py

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

apps/api/src/services/docker.py

@@ -1,556 +0,0 @@
-"""Docker service for managing tool instances."""
-
-import os
-import re
-import subprocess
-import time
-from pathlib import Path
-from typing import Any
-
-
-def render_compose_template(template: str, variables: dict[str, Any]) -> str:
-    """Render a Docker Compose template with variable substitution.
-
-    Args:
-        template: The compose template string
-        variables: Dictionary of variable names to values
-
-    Returns:
-        Rendered compose file content
-    """
-    result = template
-    for key, value in variables.items():
-        placeholder = f"{{{{{key}}}}}"
-        result = result.replace(placeholder, str(value))
-    return result
-
-
-def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
-    """Create and return the instance directory path.
-
-    Args:
-        instance_id: Unique instance identifier
-        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
-
-    Returns:
-        Absolute path to instance directory
-    """
-    if base_path is None:
-        from src.config import Settings
-
-        base_path = Settings().instance_base_path
-    instance_dir = Path(base_path) / instance_id
-    instance_dir.mkdir(parents=True, exist_ok=True)
-    return str(instance_dir.absolute())
-
-
-def write_compose_file(instance_dir: str, content: str) -> str:
-    """Write the rendered compose file to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        content: Rendered compose content
-
-    Returns:
-        Path to the compose file
-    """
-    compose_path = Path(instance_dir) / "docker-compose.yml"
-    compose_path.write_text(content)
-    return str(compose_path)
-
-
-def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
-    """Write environment variables to a .env file.
-
-    Args:
-        instance_dir: Path to instance directory
-        env_vars: Dictionary of env var names to values
-
-    Returns:
-        Path to the env file
-    """
-    env_path = Path(instance_dir) / ".env"
-    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
-    env_path.write_text("\n".join(lines) + "\n")
-    return str(env_path)
-
-
-def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
-    """Write config files to the instance directory.
-
-    Args:
-        instance_dir: Path to instance directory
-        files: Dictionary of file paths (relative to instance dir) to content
-    """
-    instance_path = Path(instance_dir)
-    for file_path, content in files.items():
-        # Ensure the path is within the instance directory (security)
-        full_path = instance_path / file_path
-        try:
-            full_path.resolve().relative_to(instance_path.resolve())
-        except ValueError:
-            raise ValueError(f"File path '{file_path}' escapes instance directory")
-
-        full_path.parent.mkdir(parents=True, exist_ok=True)
-        full_path.write_text(content)
-
-
-def execute_compose_command(
-    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
-) -> tuple[int, str, str]:
-    """Execute a docker compose command.
-
-    Args:
-        compose_path: Path to docker-compose.yml
-        action: The compose action (up, down, start, stop, restart)
-        timeout: Command timeout in seconds
-        env_file: Optional path to .env file for environment variables
-
-    Returns:
-        Tuple of (returncode, stdout, stderr)
-    """
-    instance_dir = Path(compose_path).parent
-
-    cmd = ["docker", "compose", "-f", compose_path]
-
-    if env_file:
-        cmd.extend(["--env-file", env_file])
-
-    if action == "up":
-        cmd.extend(["up", "-d"])
-    elif action == "down":
-        cmd.extend(["down", "-v"])
-    elif action in ("start", "stop", "restart"):
-        cmd.append(action)
-    else:
-        raise ValueError(f"Unknown compose action: {action}")
-
-    result = subprocess.run(
-        cmd,
-        cwd=str(instance_dir),
-        capture_output=True,
-        text=True,
-        timeout=timeout,
-    )
-
-    return result.returncode, result.stdout, result.stderr
-
-
-def get_container_id(instance_name: str) -> str | None:
-    """Get the container ID for a compose service.
-
-    Searches all containers including stopped/exited ones.
-
-    Args:
-        instance_name: The service name in compose
-
-    Returns:
-        Container ID or None if not found
-    """
-    # Docker container names are lowercase internally; normalize to ensure match
-    result = subprocess.run(
-        ["docker", "ps", "-a", "-q", "--filter", f"name={instance_name.lower()}"],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
-    return None
-
-
-def get_container_name(instance_name: str) -> str | None:
-    """Get the full container name for a compose service.
-
-    Searches all containers including stopped/exited ones.
-
-    Args:
-        instance_name: The service name in compose
-
-    Returns:
-        Container name or None if not found
-    """
-    # Docker container names are lowercase internally; normalize to ensure match
-    result = subprocess.run(
-        [
-            "docker",
-            "ps",
-            "-a",
-            "--format",
-            "{{.Names}}",
-            "--filter",
-            f"name={instance_name.lower()}",
-        ],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0 and result.stdout.strip():
-        return result.stdout.strip().split("\n")[0]
-    return None
-
-
-def connect_container_to_network(
-    container_name: str, network_name: str = "backend"
-) -> bool:
-    """Connect a Docker container to an existing network.
-
-    Args:
-        container_name: Name or ID of the container
-        network_name: Name of the Docker network (default: backend)
-
-    Returns:
-        True if successful, False otherwise
-    """
-    result = subprocess.run(
-        ["docker", "network", "connect", network_name, container_name],
-        capture_output=True,
-        text=True,
-    )
-    return result.returncode == 0
-
-
-def get_container_status(container_id: str) -> dict[str, Any]:
-    """Get the status of a Docker container.
-
-    Args:
-        container_id: Docker container ID
-
-    Returns:
-        Dict with 'status' (running, exited, restarting, not_found),
-        'exit_code' (int or None), and 'health' (health status or None)
-    """
-    result = subprocess.run(
-        [
-            "docker",
-            "inspect",
-            "-f",
-            "{{.State.Status}}|{{.State.ExitCode}}|{{if .State.Health}}{{.State.Health.Status}}{{else}}none{{end}}",
-            container_id,
-        ],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode != 0:
-        return {"status": "not_found", "exit_code": None, "health": None}
-
-    parts = result.stdout.strip().split("|")
-    status = parts[0] if parts else "unknown"
-    exit_code = int(parts[1]) if len(parts) > 1 and parts[1].isdigit() else None
-    health = parts[2] if len(parts) > 2 and parts[2] != "none" else None
-
-    return {"status": status, "exit_code": exit_code, "health": health}
-
-
-def wait_for_container_running(
-    container_id: str, timeout: int = 30, interval: float = 2.0
-) -> dict[str, Any]:
-    """Wait for a container to reach the running state.
-
-    Polls docker inspect until the container status is "running" or timeout.
-
-    Args:
-        container_id: Docker container ID
-        timeout: Maximum seconds to wait
-        interval: Seconds between polls
-
-    Returns:
-        Dict with 'success' (bool), 'status' (str), 'exit_code' (int or None),
-        and 'waited_seconds' (float)
-    """
-
-    start_time = time.time()
-
-    while time.time() - start_time < timeout:
-        info = get_container_status(container_id)
-
-        if info["status"] == "running":
-            return {
-                "success": True,
-                "status": "running",
-                "exit_code": None,
-                "waited_seconds": time.time() - start_time,
-            }
-
-        if info["status"] == "exited":
-            return {
-                "success": False,
-                "status": "exited",
-                "exit_code": info["exit_code"],
-                "waited_seconds": time.time() - start_time,
-            }
-
-        if info["status"] == "not_found":
-            return {
-                "success": False,
-                "status": "not_found",
-                "exit_code": None,
-                "waited_seconds": time.time() - start_time,
-            }
-
-        time.sleep(interval)
-
-    # Timeout reached
-    info = get_container_status(container_id)
-    return {
-        "success": False,
-        "status": info["status"],
-        "exit_code": info["exit_code"],
-        "waited_seconds": time.time() - start_time,
-    }
-
-
-def get_container_logs(container_id: str, tail: int = 100) -> str:
-    """Get the logs of a Docker container.
-
-    Args:
-        container_id: Docker container ID
-        tail: Number of lines to return
-
-    Returns:
-        Container logs
-    """
-    result = subprocess.run(
-        ["docker", "logs", "--tail", str(tail), container_id],
-        capture_output=True,
-        text=True,
-    )
-
-    if result.returncode == 0:
-        return result.stdout
-    return f"Failed to get logs: {result.stderr}"
-
-
-def find_free_port(start: int = 10000, end: int = 20000) -> int:
-    """Find a free TCP port in the given range.
-
-    Args:
-        start: Start of port range
-        end: End of port range
-
-    Returns:
-        Free port number
-    """
-    import socket
-
-    for port in range(start, end):
-        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-            if s.connect_ex(("localhost", port)) != 0:
-                return port
-
-    raise RuntimeError(f"No free port found in range {start}-{end}")
-
-
-def start_cloudflared_tunnel(
-    container_name: str, port: int, timeout: int = 30
-) -> dict[str, str]:
-    """Start a temporary Cloudflare tunnel for a container.
-
-    Uses 'cloudflared tunnel --url' to create a temporary tunnel
-    with a random trycloudflare.com URL.
-
-    Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        timeout: Maximum seconds to wait for tunnel URL
-
-    Returns:
-        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
-    """
-    import subprocess
-    import logging
-
-    logger = logging.getLogger(__name__)
-
-    # First verify the container is accessible
-    logger.info("Checking connectivity to %s:%d...", container_name, port)
-    for attempt in range(10):
-        check = subprocess.run(
-            [
-                "curl",
-                "-s",
-                "-o",
-                "/dev/null",
-                "-w",
-                "%{http_code}",
-                f"http://{container_name}:{port}",
-            ],
-            capture_output=True,
-            text=True,
-            timeout=5,
-        )
-        logger.info(
-            "Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip()
-        )
-        if check.returncode == 0:
-            break
-        time.sleep(1)
-    else:
-        logger.warning(
-            "Container %s:%d not responding to curl checks", container_name, port
-        )
-
-    # Run cloudflared in background, capture output
-    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
-    proc = subprocess.Popen(
-        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        text=True,
-    )
-
-    # Wait for the URL to appear in output
-    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
-    start_time = time.time()
-    url = None
-
-    if proc.stdout is None:
-        proc.terminate()
-        proc.wait(timeout=5)
-        raise RuntimeError("Failed to capture cloudflared output")
-
-    while time.time() - start_time < timeout:
-        # Read available output
-        import select
-
-        readable, _, _ = select.select([proc.stdout], [], [], 1.0)
-        if readable:
-            line = proc.stdout.readline()
-            if line:
-                match = url_pattern.search(line)
-                if match:
-                    url = match.group(0)
-                    break
-
-    if not url:
-        proc.terminate()
-        proc.wait(timeout=5)
-        raise RuntimeError(
-            f"Failed to get tunnel URL within {timeout}s. "
-            f"cloudflared output may contain errors."
-        )
-
-    return {"url": url, "pid": str(proc.pid)}
-
-
-def stop_cloudflared_tunnel(pid: str) -> None:
-    """Stop a cloudflared tunnel process.
-
-    Args:
-        pid: Process ID of the cloudflared tunnel
-    """
-    import signal
-
-    try:
-        os.kill(int(pid), signal.SIGTERM)
-    except ProcessLookupError:
-        pass  # Already stopped
-
-
-def recreate_tunnel(
-    container_name: str, port: int, old_pid: str | None = None
-) -> dict[str, str]:
-    """Recreate a temporary Cloudflare tunnel.
-
-    Stops the old tunnel (if pid provided) and starts a new one.
-
-    Args:
-        container_name: Name of the Docker container to tunnel to
-        port: Port number the container listens on
-        old_pid: Optional PID of the old tunnel process to stop
-
-    Returns:
-        Dict with 'url' and 'pid' for the new tunnel
-    """
-    if old_pid:
-        stop_cloudflared_tunnel(old_pid)
-
-    return start_cloudflared_tunnel(container_name, port)
-
-
-def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
-    """Check if a tunnel URL is healthy with smart error classification.
-
-    Args:
-        url: The tunnel URL to check
-        timeout: Request timeout in seconds
-
-    Returns:
-        Dict with 'tunnel_status' (healthy, unreachable, error_response, not_applicable),
-        'status_code' (int or None), 'healthy' (bool), and 'error' (str or None)
-    """
-    import subprocess
-
-    try:
-        result = subprocess.run(
-            [
-                "curl",
-                "-s",
-                "-o",
-                "/dev/null",
-                "-w",
-                "%{http_code}",
-                "--max-time",
-                str(timeout),
-                url,
-            ],
-            capture_output=True,
-            text=True,
-            timeout=timeout + 5,
-        )
-        status_code = int(result.stdout.strip())
-
-        if 200 <= status_code < 400:
-            return {
-                "tunnel_status": "healthy",
-                "status_code": status_code,
-                "healthy": True,
-                "error": None,
-            }
-        elif status_code in (502, 503, 504):
-            # Application error, not tunnel error
-            return {
-                "tunnel_status": "error_response",
-                "status_code": status_code,
-                "healthy": False,
-                "error": f"Application returned HTTP {status_code}",
-            }
-        else:
-            return {
-                "tunnel_status": "error_response",
-                "status_code": status_code,
-                "healthy": False,
-                "error": f"HTTP {status_code}",
-            }
-    except subprocess.TimeoutExpired:
-        return {
-            "tunnel_status": "unreachable",
-            "status_code": None,
-            "healthy": False,
-            "error": "Tunnel request timed out",
-        }
-    except (ValueError, Exception) as e:
-        error_str = str(e).lower()
-        # Classify connection errors
-        if any(
-            err in error_str
-            for err in [
-                "connection refused",
-                "econnrefused",
-                "could not resolve",
-                "nodename",
-            ]
-        ):
-            return {
-                "tunnel_status": "unreachable",
-                "status_code": None,
-                "healthy": False,
-                "error": f"Tunnel unreachable: {e}",
-            }
-        return {
-            "tunnel_status": "unreachable",
-            "status_code": None,
-            "healthy": False,
-            "error": str(e),
-        }

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

@@ -0,0 +1,43 @@
+"""Docker services for container and tunnel management."""
+
+from .compose import (
+    ensure_instance_directory,
+    execute_compose_command,
+    render_compose_template,
+    write_compose_file,
+    write_env_file,
+)
+from .config_staging import write_config_files
+from .container import (
+    connect_container_to_network,
+    find_free_port,
+    get_container_id,
+    get_container_logs,
+    get_container_name,
+    get_container_status,
+)
+from .tunnel import (
+    check_tunnel_health,
+    recreate_tunnel,
+    start_cloudflared_tunnel,
+    stop_cloudflared_tunnel,
+)
+
+__all__ = [
+    "render_compose_template",
+    "ensure_instance_directory",
+    "write_compose_file",
+    "write_env_file",
+    "execute_compose_command",
+    "write_config_files",
+    "get_container_id",
+    "get_container_name",
+    "connect_container_to_network",
+    "get_container_status",
+    "get_container_logs",
+    "find_free_port",
+    "start_cloudflared_tunnel",
+    "stop_cloudflared_tunnel",
+    "recreate_tunnel",
+    "check_tunnel_health",
+]

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

@@ -0,0 +1,237 @@
+"""Docker Compose file generation and command execution."""
+
+import re
+import subprocess
+import uuid
+from pathlib import Path
+from typing import Any
+
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.config_profile import ConfigProfile
+from src.models.tool_instance import ToolInstance
+from src.services.profile_resolver import resolve_profile
+
+
+def _sanitize_name(name: str) -> str:
+    """Sanitize a string for use in Docker/container names."""
+    sanitized = re.sub(r"[^a-z0-9-]", "-", name.lower())
+    sanitized = re.sub(r"-+", "-", sanitized)
+    return sanitized.strip("-")
+
+
+async def _generate_instance_name(
+    session: AsyncSession,
+    project_name: str,
+    tool_type_name: str,
+) -> str:
+    """Generate a unique instance name: project-tool-NUM."""
+    base = f"{_sanitize_name(project_name)}-{_sanitize_name(tool_type_name)}"
+    base = base.strip("-") or "instance"
+    result = await session.execute(
+        select(ToolInstance.name).where(ToolInstance.name.like(f"{base}-%"))
+    )
+    names = result.scalars().all()
+    max_num = 0
+    for name in names:
+        parts = name.rsplit("-", 1)
+        if len(parts) == 2 and parts[0] == base and parts[1].isdigit():
+            max_num = max(max_num, int(parts[1]))
+    return f"{base}-{max_num + 1:03d}"
+
+
+def _modify_compose_file(
+    compose_path: str,
+    port_override: int | None = None,
+    start_command: str | None = None,
+    working_directory: str | None = None,
+    extra_volumes: list[dict] | None = None,
+) -> None:
+    """Modify compose file with runtime overrides."""
+    import yaml
+
+    compose_file = Path(compose_path)
+    content = compose_file.read_text()
+    compose_data = yaml.safe_load(content)
+
+    if not compose_data or "services" not in compose_data:
+        return
+
+    for service_name, service_config in compose_data["services"].items():
+        if port_override and "ports" in service_config:
+            for i, port_mapping in enumerate(service_config["ports"]):
+                if isinstance(port_mapping, str) and ":" in port_mapping:
+                    _host_port, container_port = port_mapping.split(":", 1)
+                    service_config["ports"][i] = f"{port_override}:{container_port}"
+                    break
+
+        if start_command:
+            service_config["command"] = start_command
+
+        if working_directory:
+            service_config["working_dir"] = working_directory
+
+        if extra_volumes:
+            if "volumes" not in service_config:
+                service_config["volumes"] = []
+            for vol in extra_volumes:
+                source = vol.get("source", "")
+                target = vol.get("target", "")
+                vol_type = vol.get("type", "bind")
+                if vol_type == "bind":
+                    service_config["volumes"].append(f"{source}:{target}")
+                else:
+                    service_config["volumes"].append(f"{source}:{target}:{vol_type}")
+
+        break
+
+    compose_file.write_text(yaml.dump(compose_data, default_flow_style=False))
+
+
+async def _apply_resolved_profile(
+    profile: ConfigProfile,
+    instance_dir: str,
+    env_vars: dict[str, str],
+    port_override: int | None,
+    start_command: str | None,
+    working_directory: str | None,
+    extra_volumes: list[dict],
+) -> tuple[dict[str, str], int | None, str | None, str | None, list[dict]]:
+    """Resolve a profile and apply its output to instance configuration."""
+    resolved = resolve_profile(profile)
+
+    if resolved.environment_variables:
+        env_vars.update(resolved.environment_variables)
+
+    if resolved.runtime_hints.start_command is not None:
+        start_command = resolved.runtime_hints.start_command
+    if resolved.runtime_hints.working_directory is not None:
+        working_directory = resolved.runtime_hints.working_directory
+    if resolved.runtime_hints.port is not None:
+        port_override = resolved.runtime_hints.port
+
+    for target_path, mount in resolved.mounts.items():
+        safe_name = target_path.strip("/").replace("/", "_")
+        mount_dir = Path(instance_dir) / "mounts" / safe_name
+        mount_dir.mkdir(parents=True, exist_ok=True)
+
+        for rel_path, content in mount.files.items():
+            file_path = mount_dir / rel_path
+            file_path.parent.mkdir(parents=True, exist_ok=True)
+            file_path.write_text(content)
+
+        extra_volumes.append({
+            "source": str(mount_dir),
+            "target": target_path,
+            "type": mount.mode,
+        })
+
+    return env_vars, port_override, start_command, working_directory, extra_volumes
+
+
+def render_compose_template(template: str, variables: dict[str, Any]) -> str:
+    """Render a Docker Compose template with variable substitution.
+
+    Args:
+        template: The compose template string
+        variables: Dictionary of variable names to values
+
+    Returns:
+        Rendered compose file content
+    """
+    result = template
+    for key, value in variables.items():
+        placeholder = f"{{{{{key}}}}}"
+        result = result.replace(placeholder, str(value))
+    return result
+
+
+def ensure_instance_directory(instance_id: str, base_path: str | None = None) -> str:
+    """Create and return the instance directory path.
+
+    Args:
+        instance_id: Unique instance identifier
+        base_path: Base directory for all instances (defaults to Settings.instance_base_path)
+
+    Returns:
+        Absolute path to instance directory
+    """
+    if base_path is None:
+        from src.config import Settings
+        base_path = Settings().instance_base_path
+    instance_dir = Path(base_path) / instance_id
+    instance_dir.mkdir(parents=True, exist_ok=True)
+    return str(instance_dir.absolute())
+
+
+def write_compose_file(instance_dir: str, content: str) -> str:
+    """Write the rendered compose file to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        content: Rendered compose content
+
+    Returns:
+        Path to the compose file
+    """
+    compose_path = Path(instance_dir) / "docker-compose.yml"
+    compose_path.write_text(content)
+    return str(compose_path)
+
+
+def write_env_file(instance_dir: str, env_vars: dict[str, str]) -> str:
+    """Write environment variables to a .env file.
+
+    Args:
+        instance_dir: Path to instance directory
+        env_vars: Dictionary of env var names to values
+
+    Returns:
+        Path to the env file
+    """
+    env_path = Path(instance_dir) / ".env"
+    lines = [f'{key}="{value}"' for key, value in env_vars.items()]
+    env_path.write_text("\n".join(lines) + "\n")
+    return str(env_path)
+
+
+def execute_compose_command(
+    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
+) -> tuple[int, str, str]:
+    """Execute a docker compose command.
+
+    Args:
+        compose_path: Path to docker-compose.yml
+        action: The compose action (up, down, start, stop, restart)
+        timeout: Command timeout in seconds
+        env_file: Optional path to .env file for environment variables
+
+    Returns:
+        Tuple of (returncode, stdout, stderr)
+    """
+    instance_dir = Path(compose_path).parent
+
+    cmd = ["docker", "compose", "-f", compose_path]
+
+    if env_file:
+        cmd.extend(["--env-file", env_file])
+
+    if action == "up":
+        cmd.extend(["up", "-d"])
+    elif action == "down":
+        cmd.extend(["down", "-v"])
+    elif action in ("start", "stop", "restart"):
+        cmd.append(action)
+    else:
+        raise ValueError(f"Unknown compose action: {action}")
+
+    result = subprocess.run(
+        cmd,
+        cwd=str(instance_dir),
+        capture_output=True,
+        text=True,
+        timeout=timeout,
+    )
+
+    return result.returncode, result.stdout, result.stderr

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

@@ -0,0 +1,22 @@
+"""Config file staging for Docker instances."""
+
+from pathlib import Path
+
+def write_config_files(instance_dir: str, files: dict[str, str]) -> None:
+    """Write config files to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        files: Dictionary of file paths (relative to instance dir) to content
+    """
+    instance_path = Path(instance_dir)
+    for file_path, content in files.items():
+        # Ensure the path is within the instance directory (security)
+        full_path = instance_path / file_path
+        try:
+            full_path.resolve().relative_to(instance_path.resolve())
+        except ValueError:
+            raise ValueError(f"File path '{file_path}' escapes instance directory")
+
+        full_path.parent.mkdir(parents=True, exist_ok=True)
+        full_path.write_text(content)

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

@@ -0,0 +1,121 @@
+"""Docker container lifecycle and query operations."""
+
+import socket
+import subprocess
+
+
+def get_container_id(instance_name: str) -> str | None:
+    """Get the container ID for a compose service.
+
+    Args:
+        instance_name: The service name in compose
+
+    Returns:
+        Container ID or None if not found
+    """
+    result = subprocess.run(
+        ["docker", "ps", "-q", "--filter", f"name={instance_name}"],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0 and result.stdout.strip():
+        return result.stdout.strip().split("\n")[0]
+    return None
+
+
+def get_container_name(instance_name: str) -> str | None:
+    """Get the full container name for a compose service.
+
+    Args:
+        instance_name: The service name in compose
+
+    Returns:
+        Container name or None if not found
+    """
+    result = subprocess.run(
+        ["docker", "ps", "--format", "{{.Names}}", "--filter", f"name={instance_name}"],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0 and result.stdout.strip():
+        return result.stdout.strip().split("\n")[0]
+    return None
+
+
+def connect_container_to_network(container_name: str, network_name: str = "backend") -> bool:
+    """Connect a Docker container to an existing network.
+
+    Args:
+        container_name: Name or ID of the container
+        network_name: Name of the Docker network (default: backend)
+
+    Returns:
+        True if successful, False otherwise
+    """
+    result = subprocess.run(
+        ["docker", "network", "connect", network_name, container_name],
+        capture_output=True,
+        text=True,
+    )
+    return result.returncode == 0
+
+
+def get_container_status(container_id: str) -> str:
+    """Get the status of a Docker container.
+
+    Args:
+        container_id: Docker container ID
+
+    Returns:
+        Container status string (running, exited, etc.)
+    """
+    result = subprocess.run(
+        ["docker", "inspect", "-f", "{{.State.Status}}", container_id],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0:
+        return result.stdout.strip()
+    return "unknown"
+
+
+def get_container_logs(container_id: str, tail: int = 100) -> str:
+    """Get the logs of a Docker container.
+
+    Args:
+        container_id: Docker container ID
+        tail: Number of lines to return
+
+    Returns:
+        Container logs
+    """
+    result = subprocess.run(
+        ["docker", "logs", "--tail", str(tail), container_id],
+        capture_output=True,
+        text=True,
+    )
+
+    if result.returncode == 0:
+        return result.stdout
+    return f"Failed to get logs: {result.stderr}"
+
+
+def find_free_port(start: int = 10000, end: int = 20000) -> int:
+    """Find a free TCP port in the given range.
+
+    Args:
+        start: Start of port range
+        end: End of port range
+
+    Returns:
+        Free port number
+    """
+    for port in range(start, end):
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+            if s.connect_ex(("localhost", port)) != 0:
+                return port
+
+    raise RuntimeError(f"No free port found in range {start}-{end}")

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

@@ -0,0 +1,146 @@
+"""Cloudflare tunnel management for Docker instances."""
+
+import logging
+import os
+import re
+import signal
+import subprocess
+import time
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+
+def start_cloudflared_tunnel(
+    container_name: str, port: int, timeout: int = 30
+) -> dict[str, str]:
+    """Start a temporary Cloudflare tunnel for a container.
+
+    Uses 'cloudflared tunnel --url' to create a temporary tunnel
+    with a random trycloudflare.com URL.
+
+    Args:
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
+        timeout: Maximum seconds to wait for tunnel URL
+
+    Returns:
+        Dict with 'url' (the public tunnel URL) and 'pid' (process ID)
+    """
+    import select as sel
+
+    # First verify the container is accessible
+    logger.info("Checking connectivity to %s:%d...", container_name, port)
+    for attempt in range(10):
+        check = subprocess.run(
+            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
+             f"http://{container_name}:{port}"],
+            capture_output=True,
+            text=True,
+            timeout=5,
+        )
+        logger.info("Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip())
+        if check.returncode == 0:
+            break
+        time.sleep(1)
+    else:
+        logger.warning("Container %s:%d not responding to curl checks", container_name, port)
+
+    # Run cloudflared in background, capture output
+    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
+    proc = subprocess.Popen(
+        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        text=True,
+    )
+
+    # Wait for the URL to appear in output
+    url_pattern = re.compile(r"https://[a-z0-9-]+\.trycloudflare\.com")
+    start_time = time.time()
+    url = None
+
+    while time.time() - start_time < timeout:
+        # Read available output
+        readable, _, _ = sel.select([proc.stdout], [], [], 1.0)
+        if readable:
+            line = proc.stdout.readline()
+            if line:
+                match = url_pattern.search(line)
+                if match:
+                    url = match.group(0)
+                    break
+
+    if not url:
+        proc.terminate()
+        proc.wait(timeout=5)
+        raise RuntimeError(
+            f"Failed to get tunnel URL within {timeout}s. "
+            f"cloudflared output may contain errors."
+        )
+
+    return {"url": url, "pid": str(proc.pid)}
+
+
+def stop_cloudflared_tunnel(pid: str) -> None:
+    """Stop a cloudflared tunnel process.
+
+    Args:
+        pid: Process ID of the cloudflared tunnel
+    """
+    try:
+        os.kill(int(pid), signal.SIGTERM)
+    except ProcessLookupError:
+        pass  # Already stopped
+
+
+def recreate_tunnel(
+    container_name: str, port: int, old_pid: str | None = None
+) -> dict[str, str]:
+    """Recreate a temporary Cloudflare tunnel.
+
+    Stops the old tunnel (if pid provided) and starts a new one.
+
+    Args:
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
+        old_pid: Optional PID of the old tunnel process to stop
+
+    Returns:
+        Dict with 'url' and 'pid' for the new tunnel
+    """
+    if old_pid:
+        stop_cloudflared_tunnel(old_pid)
+
+    return start_cloudflared_tunnel(container_name, port)
+
+
+def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:
+    """Check if a tunnel URL is healthy.
+
+    Args:
+        url: The tunnel URL to check
+        timeout: Request timeout in seconds
+
+    Returns:
+        Dict with 'healthy' (bool) and 'status_code' (int or None)
+    """
+    try:
+        result = subprocess.run(
+            ["curl", "-s", "-o", "/dev/null", "-w", "%{http_code}",
+             "--max-time", str(timeout), url],
+            capture_output=True,
+            text=True,
+            timeout=timeout + 5,
+        )
+        status_code = int(result.stdout.strip())
+        return {
+            "healthy": 200 <= status_code < 400,
+            "status_code": status_code,
+        }
+    except (ValueError, subprocess.TimeoutExpired, Exception) as e:
+        return {
+            "healthy": False,
+            "status_code": None,
+            "error": str(e),
+        }

apps/api/src/services/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,
     ]
 

apps/api/src/services/event_bus.py

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

apps/api/src/services/file_service.py

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

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

@@ -0,0 +1 @@
+"""Git services package."""

apps/api/src/services/git/control.py

@@ -0,0 +1,196 @@
+"""Git control operations with repo validation."""
+
+import logging
+import os
+import uuid
+
+from fastapi import HTTPException, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.git_repository import GitRepository
+from src.models.user import User
+from src.schemas.git_repository import (
+    BranchCreateRequest,
+    CheckoutRequest,
+    CommitRequest,
+    FetchResponse,
+    MergeRequest,
+    MergeResponse,
+    PullResponse,
+    PushResponse,
+    StatusResponse,
+)
+from src.services.git.repository import ensure_repo_on_disk, get_repo_and_validate
+from src.utils.git_control import (
+    checkout_branch,
+    commit_changes,
+    create_branch,
+    delete_branch,
+    fetch,
+    get_status,
+    merge,
+    pull,
+    push,
+)
+
+logger = logging.getLogger(__name__)
+
+
+async def get_status_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+) -> StatusResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        result = get_status(repo.path)
+        return StatusResponse(
+            branch=result.branch,
+            modified=result.modified,
+            added=result.added,
+            deleted=result.deleted,
+            untracked=result.untracked,
+            renamed=result.renamed,
+            ahead=result.ahead,
+            behind=result.behind,
+        )
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def create_branch_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: BranchCreateRequest,
+) -> dict:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        create_branch(repo.path, data.name, data.base_branch)
+        return {"message": f"Branch '{data.name}' created", "branch": data.name}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def delete_branch_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch_name: str,
+    force: bool = False,
+) -> dict:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        delete_branch(repo.path, branch_name, force)
+        return {"message": f"Branch '{branch_name}' deleted"}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def checkout_branch_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: CheckoutRequest,
+) -> dict:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        checkout_branch(repo.path, data.branch)
+        return {"message": f"Checked out branch '{data.branch}'", "branch": data.branch}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def commit_changes_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: CommitRequest,
+    user: User,
+) -> dict:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    author_name = user.name or "Unknown"
+    author_email = user.email or "unknown@example.com"
+    try:
+        commit_hash = commit_changes(
+            repo_path=repo.path,
+            message=data.message,
+            author_name=author_name,
+            author_email=author_email,
+            files=data.files,
+        )
+        return {"commit_hash": commit_hash, "message": data.message}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def fetch_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+) -> FetchResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        fetch(repo.path)
+        return FetchResponse(message="Fetched from remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def pull_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str | None = None,
+) -> PullResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        pull(repo.path, branch)
+        return PullResponse(message="Pulled from remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def push_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str | None = None,
+) -> PushResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        push(repo.path, branch)
+        return PushResponse(message="Pushed to remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def merge_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: MergeRequest,
+) -> MergeResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        commit_hash = merge(
+            repo_path=repo.path,
+            source_branch=data.source_branch,
+            target_branch=data.target_branch,
+            message=data.message,
+        )
+        return MergeResponse(
+            commit_hash=commit_hash,
+            message=data.message or f"Merge {data.source_branch}",
+        )
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))

apps/api/src/services/git/files.py

@@ -0,0 +1,150 @@
+"""Git file operations with repo validation."""
+
+import logging
+import uuid
+
+from fastapi import HTTPException, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.git_repository import GitRepository
+from src.models.user import User
+from src.schemas.git_repository import (
+    FileContentResponse,
+    FileListResponse,
+    FileUpdateRequest,
+    FileUpdateResponse,
+)
+from src.services.git.repository import ensure_repo_on_disk, get_repo_and_validate
+from src.utils.git_files import (
+    commit_file,
+    get_file_content,
+    list_branches,
+    list_tree,
+)
+
+logger = logging.getLogger(__name__)
+
+
+async def list_files(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str = "main",
+    path: str = "",
+) -> FileListResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        entries = list_tree(repo.path, branch=branch, path=path)
+        return FileListResponse(
+            path=path,
+            branch=branch,
+            entries=[
+                {
+                    "name": e.name,
+                    "type": e.type,
+                    "path": e.path,
+                    "size": e.size,
+                    "mode": e.mode,
+                    "last_commit": e.last_commit,
+                }
+                for e in entries
+            ],
+        )
+    except RuntimeError as e:
+        logger.error(
+            "Failed to list files for repo %s (path=%s, branch=%s): %s",
+            repo_id,
+            path,
+            branch,
+            str(e),
+            exc_info=True,
+        )
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def get_file(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str,
+    path: str,
+) -> FileContentResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        file_content = get_file_content(repo.path, branch=branch, path=path)
+        return FileContentResponse(
+            path=file_content.path,
+            branch=file_content.branch,
+            content=file_content.content,
+            size=file_content.size,
+            encoding=file_content.encoding,
+            language=file_content.language,
+            is_binary=file_content.is_binary,
+            last_commit=file_content.last_commit,
+        )
+    except FileNotFoundError:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def update_file(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: FileUpdateRequest,
+    user: User,
+) -> FileUpdateResponse:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    author_name = user.name or "Unknown"
+    author_email = user.email or "unknown@example.com"
+    try:
+        commit_hash = commit_file(
+            repo_path=repo.path,
+            branch=data.branch,
+            path=data.path,
+            content=data.content,
+            commit_message=data.commit_message,
+            author_name=author_name,
+            author_email=author_email,
+        )
+        return FileUpdateResponse(
+            commit_hash=commit_hash,
+            message=data.commit_message,
+            branch=data.branch,
+        )
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+async def list_branches_with_validation(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+) -> dict:
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        branches, default_branch = list_branches(repo.path)
+        return {
+            "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_400_BAD_REQUEST, detail=str(e))

apps/api/src/services/git/repository.py

@@ -0,0 +1,211 @@
+"""Repository lifecycle and path helpers."""
+
+import logging
+import os
+import shutil
+import subprocess
+import uuid
+
+from fastapi import HTTPException, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.config import Settings
+from src.models.git_repository import GitRepository
+from src.models.project import Project
+from src.models.user import User
+from src.schemas.git_repository import GitRepositoryCreate
+from src.utils.git_url_parser import parse_git_url
+
+logger = logging.getLogger(__name__)
+
+
+def _get_repo_path(user_id: uuid.UUID, project_id: uuid.UUID, name: str) -> str:
+    """Generate the filesystem path for a repository."""
+    base = Settings().repo_base_path or "/data/repos"
+    return os.path.join(base, str(user_id), str(project_id), f"{name}.git")
+
+
+def _build_provider_clone_url(owner: str, repo: str) -> str:
+    """Build the SSH clone URL for the fixed git provider."""
+    return f"git@git.commumedia.org:{owner}/{repo}.git"
+
+
+def _preflight_remote_repository(remote_url: str) -> None:
+    """Verify a remote repository is reachable before cloning."""
+    try:
+        result = subprocess.run(
+            ["git", "ls-remote", remote_url],
+            capture_output=True,
+            text=True,
+            timeout=60,
+        )
+    except subprocess.TimeoutExpired:
+        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")
+
+    if result.returncode != 0:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail="repository not found or inaccessible",
+        )
+
+
+def _clone_working_repository(remote_url: str, repo_path: str) -> None:
+    try:
+        result = subprocess.run(
+            ["git", "clone", remote_url, repo_path],
+            capture_output=True,
+            text=True,
+            timeout=300,
+        )
+    except subprocess.TimeoutExpired:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="clone operation timed out")
+    except FileNotFoundError:
+        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+
+    if result.returncode != 0:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"failed to clone repository: {result.stderr}",
+        )
+
+
+def _init_working_repository(repo_path: str) -> None:
+    try:
+        result = subprocess.run(
+            ["git", "init", "-b", "main", repo_path],
+            capture_output=True,
+            text=True,
+        )
+    except FileNotFoundError:
+        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="git command not found")
+
+    if result.returncode == 0:
+        return
+
+    fallback = subprocess.run(
+        ["git", "init", repo_path],
+        capture_output=True,
+        text=True,
+    )
+    if fallback.returncode != 0:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"failed to initialize repository: {fallback.stderr}",
+        )
+
+    ref_result = subprocess.run(
+        ["git", "-C", repo_path, "symbolic-ref", "HEAD", "refs/heads/main"],
+        capture_output=True,
+        text=True,
+    )
+    if ref_result.returncode != 0:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"failed to set initial branch: {ref_result.stderr}",
+        )
+
+
+async def get_repo_and_validate(
+    session: AsyncSession,
+    repo_id: uuid.UUID,
+    project_id: uuid.UUID,
+) -> GitRepository:
+    """Fetch a repository and validate ownership + disk presence."""
+    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")
+    return repo
+
+
+def ensure_repo_on_disk(repo: GitRepository) -> None:
+    """Raise 404 if the repository is not present on disk."""
+    if not os.path.exists(repo.path):
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
+
+
+async def create_repository(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+    data: GitRepositoryCreate,
+    user: User,
+) -> GitRepository:
+    """Create a new git repository (clone or init)."""
+    # Check for duplicate name
+    existing = await session.execute(
+        select(GitRepository).where(
+            GitRepository.project_id == project_id,
+            GitRepository.name == data.name,
+        )
+    )
+    if existing.scalar_one_or_none():
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+
+    # Validate and potentially correct the URL
+    remote_url = data.remote_url
+    if remote_url and not data.force_original_url:
+        parse_result = parse_git_url(remote_url)
+        if parse_result["needs_parsing"] and parse_result["base_url"]:
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail={
+                    "message": "The provided URL appears to be a browser URL, not a git clone URL",
+                    "suggested_url": parse_result["base_url"],
+                    "original_url": remote_url,
+                    "error_code": "URL_NEEDS_PARSING",
+                },
+            )
+        if parse_result["base_url"]:
+            remote_url = parse_result["base_url"]
+
+    if remote_url:
+        _preflight_remote_repository(remote_url)
+
+    repo_path = _get_repo_path(user.id, project_id, data.name)
+    os.makedirs(os.path.dirname(repo_path), exist_ok=True)
+
+    if remote_url:
+        _clone_working_repository(remote_url, repo_path)
+    else:
+        _init_working_repository(repo_path)
+
+    repo = GitRepository(
+        name=data.name,
+        path=repo_path,
+        project_id=project_id,
+        owner_id=user.id,
+        is_mirror=False,
+        remote_url=remote_url,
+    )
+    session.add(repo)
+    await session.commit()
+    await session.refresh(repo)
+    return repo
+
+
+async def delete_repository(
+    session: AsyncSession,
+    repo_id: uuid.UUID,
+    project_id: uuid.UUID,
+) -> None:
+    """Delete a repository from DB and disk."""
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+
+    if os.path.exists(repo.path):
+        shutil.rmtree(repo.path)
+
+    await session.delete(repo)
+    await session.commit()
+
+
+async def list_repositories(
+    session: AsyncSession,
+    project_id: uuid.UUID,
+) -> list[GitRepository]:
+    """List all repositories in a project."""
+    result = await session.execute(
+        select(GitRepository).where(GitRepository.project_id == project_id)
+    )
+    return list(result.scalars().all())

apps/api/src/services/git_operations.py

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

apps/api/src/services/git_service.py

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

apps/api/src/services/health_monitor.py

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

apps/api/src/services/instance_lifecycle.py

@@ -0,0 +1,418 @@
+"""High-level tool instance lifecycle orchestration.
+
+Coordinates Docker compose, container, tunnel, and config staging services
+to create, start, stop, restart, and delete tool instances.
+"""
+
+import logging
+import os
+import shutil
+from datetime import datetime
+from typing import Any
+
+from fastapi import HTTPException, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.models.config_profile import ConfigProfile
+from src.models.git_repository import GitRepository
+from src.models.project import Project
+from src.models.tool_instance import ToolInstance
+from src.models.tool_type import ToolType
+from src.models.user import User
+from src.services.docker import compose as compose_svc
+from src.services.docker import config_staging
+from src.services.docker import container as container_svc
+from src.services.docker import tunnel as tunnel_svc
+from src.services.docker_build import build_image
+from src.services.readiness_probe import execute_probe
+
+logger = logging.getLogger(__name__)
+
+
+async def create_new_instance(
+    session: AsyncSession,
+    project: Project,
+    repo: GitRepository,
+    tool_type: ToolType,
+    user: User,
+    display_name: str | None,
+    selected_profile: ConfigProfile | None,
+) -> ToolInstance:
+    """Create a new tool instance record and its compose file."""
+    instance_name = await compose_svc._generate_instance_name(
+        session, project.name, tool_type.name
+    )
+    instance_dir = compose_svc.ensure_instance_directory(instance_name)
+    tool_port = container_svc.find_free_port()
+
+    compose_path = await _build_or_render_compose(
+        tool_type, instance_name, instance_dir, repo, user, project.id, tool_port
+    )
+
+    instance = ToolInstance(
+        name=instance_name,
+        display_name=display_name
+        or f"{project.name} / {repo.name} / {tool_type.display_name}",
+        tool_type_id=tool_type.id,
+        repository_id=repo.id,
+        project_id=project.id,
+        owner_id=user.id,
+        status="pending",
+        compose_path=compose_path,
+        port=tool_port,
+        selected_profile_id=selected_profile.id if selected_profile else None,
+    )
+    session.add(instance)
+    await session.commit()
+    await session.refresh(instance)
+    return instance
+
+
+async def start_existing_instance(
+    session: AsyncSession,
+    instance: ToolInstance,
+    user: User,
+    project_id: Any,
+) -> dict:
+    """Start an existing instance: stage configs, compose up, probe, tunnel."""
+    if not instance.compose_path or not os.path.exists(instance.compose_path):
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST, detail="compose file not found"
+        )
+
+    instance.status = "building"
+    await session.commit()
+
+    env_vars: dict[str, str] = {}
+    config_files: dict[str, str] = {}
+    port_override = None
+    start_command = None
+    working_directory = None
+    extra_volumes: list[dict] = []
+
+    selected_profile = None
+    if instance.selected_profile_id:
+        selected_profile = await session.get(
+            ConfigProfile, instance.selected_profile_id
+        )
+        if selected_profile and selected_profile.user_id == user.id:
+            instance_dir = os.path.dirname(instance.compose_path)
+            (
+                env_vars,
+                port_override,
+                start_command,
+                working_directory,
+                extra_volumes,
+            ) = await compose_svc._apply_resolved_profile(
+                selected_profile,
+                instance_dir,
+                env_vars,
+                port_override,
+                start_command,
+                working_directory,
+                extra_volumes,
+            )
+
+    env_file_path, extra_volumes = await _stage_configs(
+        os.path.dirname(instance.compose_path), env_vars, config_files, extra_volumes
+    )
+
+    if port_override or start_command or working_directory or extra_volumes:
+        compose_svc._modify_compose_file(
+            instance.compose_path,
+            port_override,
+            start_command,
+            working_directory,
+            extra_volumes,
+        )
+
+    returncode, _stdout, stderr = compose_svc.execute_compose_command(
+        instance.compose_path, "up", env_file=env_file_path
+    )
+    if returncode != 0:
+        instance.status = "error"
+        await session.commit()
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail=f"failed to start instance: {stderr}",
+        )
+
+    container_id = container_svc.get_container_id(instance.name)
+    if container_id:
+        instance.container_id = container_id
+    container_name = container_svc.get_container_name(instance.name)
+    if container_name:
+        instance.container_name = container_name
+        container_svc.connect_container_to_network(container_name, "backend")
+
+    instance.status = "starting"
+    instance.last_started_at = datetime.now()
+    await session.commit()
+
+    tool_type = await session.get(ToolType, instance.tool_type_id)
+    if not tool_type:
+        instance.status = "error"
+        await session.commit()
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail="tool type not found for instance",
+        )
+
+    success, probe_logs = await _run_readiness_probe(instance, tool_type)
+    if not success:
+        instance.status = "failed"
+        instance.url = None
+        instance.public_url = None
+        await session.commit()
+        return {
+            "status": "failed",
+            "error": f"Readiness probe failed: {' '.join(probe_logs)}",
+        }
+
+    instance.status = "running"
+    await session.commit()
+    await _start_tunnel_if_web(instance, tool_type)
+    await session.commit()
+
+    return {"status": instance.status, "url": instance.url}
+
+
+async def restart_existing_instance(
+    session: AsyncSession,
+    instance: ToolInstance,
+    user: User,
+    project_id: Any,
+) -> dict:
+    """Restart an instance: re-stage configs, compose restart, tunnel."""
+    if instance.tunnel_id:
+        try:
+            tunnel_svc.stop_cloudflared_tunnel(instance.tunnel_id)
+        except Exception as exc:
+            logger.warning("Failed to stop old tunnel: %s", exc)
+
+    if not instance.compose_path or not os.path.exists(instance.compose_path):
+        instance.status = "error"
+        await session.commit()
+        return {"status": instance.status}
+
+    env_vars: dict[str, str] = {}
+    config_files: dict[str, str] = {}
+    port_override = None
+    start_command = None
+    working_directory = None
+    extra_volumes: list[dict] = []
+
+    stored_profile = None
+    if instance.selected_profile_id:
+        stored_profile = await session.get(ConfigProfile, instance.selected_profile_id)
+        if stored_profile and stored_profile.user_id == user.id:
+            instance_dir = os.path.dirname(instance.compose_path)
+            (
+                env_vars,
+                port_override,
+                start_command,
+                working_directory,
+                extra_volumes,
+            ) = await compose_svc._apply_resolved_profile(
+                stored_profile,
+                instance_dir,
+                env_vars,
+                port_override,
+                start_command,
+                working_directory,
+                extra_volumes,
+            )
+
+    env_file_path, extra_volumes = await _stage_configs(
+        os.path.dirname(instance.compose_path), env_vars, config_files, extra_volumes
+    )
+
+    if port_override or start_command or working_directory or extra_volumes:
+        compose_svc._modify_compose_file(
+            instance.compose_path,
+            port_override,
+            start_command,
+            working_directory,
+            extra_volumes,
+        )
+
+    returncode, _stdout, _stderr = compose_svc.execute_compose_command(
+        instance.compose_path, "restart", env_file=env_file_path
+    )
+    if returncode != 0:
+        instance.status = "error"
+        await session.commit()
+        return {"status": instance.status}
+
+    instance.status = "running"
+    instance.last_started_at = datetime.now()
+
+    tool_type = await session.get(ToolType, instance.tool_type_id)
+    if not tool_type:
+        instance.status = "error"
+        await session.commit()
+        return {"status": instance.status}
+
+    await _start_tunnel_if_web(instance, tool_type)
+    await session.commit()
+
+    return {"status": instance.status, "url": instance.url}
+
+
+async def stop_existing_instance(session: AsyncSession, instance: ToolInstance) -> None:
+    """Stop an instance and its tunnel."""
+    if instance.tunnel_id:
+        try:
+            tunnel_svc.stop_cloudflared_tunnel(instance.tunnel_id)
+        except Exception as exc:
+            logger.warning("Failed to stop tunnel: %s", exc)
+
+    if instance.compose_path and os.path.exists(instance.compose_path):
+        compose_svc.execute_compose_command(instance.compose_path, "stop")
+
+    instance.status = "stopped"
+    instance.last_stopped_at = datetime.now()
+    instance.url = None
+    instance.public_url = None
+    instance.tunnel_id = None
+    await session.commit()
+
+
+async def delete_existing_instance(
+    session: AsyncSession, instance: ToolInstance
+) -> None:
+    """Delete an instance, its containers, and its directory."""
+    if instance.tunnel_id:
+        try:
+            tunnel_svc.stop_cloudflared_tunnel(instance.tunnel_id)
+        except Exception as exc:
+            logger.warning("Failed to stop tunnel: %s", exc)
+
+    if instance.compose_path and os.path.exists(instance.compose_path):
+        compose_svc.execute_compose_command(instance.compose_path, "down")
+        instance_dir = os.path.dirname(instance.compose_path)
+        if os.path.exists(instance_dir):
+            shutil.rmtree(instance_dir)
+
+    await session.delete(instance)
+    await session.commit()
+
+
+# ── Internal helpers ───────────────────────────────────────────────────────
+
+
+async def _build_or_render_compose(
+    tool_type: ToolType,
+    instance_name: str,
+    instance_dir: str,
+    repo: GitRepository,
+    user: User,
+    project_id: Any,
+    tool_port: int,
+) -> str:
+    """Build Dockerfile or render compose template."""
+    if tool_type.definition_type == "dockerfile":
+        image_tag = f"headquarter/{instance_name}:latest"
+        if tool_type.dockerfile_template:
+            returncode, _stdout, stderr = build_image(
+                instance_dir=instance_dir,
+                dockerfile=tool_type.dockerfile_template,
+                tag=image_tag,
+                build_context=tool_type.build_context,
+            )
+            if returncode != 0:
+                logger.error("Build failed for %s: %s", instance_name, stderr)
+                raise HTTPException(
+                    status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+                    detail=f"Failed to build Docker image: {stderr[:500]}",
+                )
+
+        compose_content = (
+            f'version: "3.8"\nservices:\n  app:\n'
+            f"    image: {image_tag}\n"
+            f"    container_name: {instance_name}\n"
+            f'    ports:\n      - "{tool_port}:{tool_type.default_port}"\n'
+            f"    volumes:\n      - {repo.path}:/workspace\n"
+            f"    restart: unless-stopped\n"
+        )
+    else:
+        variables = {
+            "REPO_PATH": repo.path,
+            "INSTANCE_NAME": instance_name,
+            "INSTANCE_ID": instance_name,
+            "TOOL_NAME": instance_name,
+            "TOOL_PORT": tool_port,
+            "USER_ID": str(user.id),
+            "PROJECT_ID": str(project_id),
+        }
+        if not tool_type.compose_template:
+            raise HTTPException(
+                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+                detail="tool type has no compose template",
+            )
+        compose_content = compose_svc.render_compose_template(
+            tool_type.compose_template, variables
+        )
+
+    compose_svc.write_compose_file(instance_dir, compose_content)
+    return os.path.join(instance_dir, "docker-compose.yml")
+
+
+async def _stage_configs(
+    instance_dir: str,
+    env_vars: dict[str, str],
+    config_files: dict[str, str],
+    extra_volumes: list[dict],
+) -> tuple[str | None, list[dict]]:
+    """Write env/config files for the resolved profile."""
+    env_file_path: str | None = None
+    if env_vars:
+        env_file_path = compose_svc.write_env_file(instance_dir, env_vars)
+    if config_files:
+        config_staging.write_config_files(instance_dir, config_files)
+
+    return env_file_path, extra_volumes
+
+
+async def _start_tunnel_if_web(instance: ToolInstance, tool_type: ToolType) -> None:
+    """Create Cloudflare tunnel for web-enabled tools."""
+    if tool_type.interface_type != "web" or not tool_type.default_port:
+        instance.url = None
+        instance.public_url = None
+        return
+
+    try:
+        tunnel_info = tunnel_svc.start_cloudflared_tunnel(
+            container_name=instance.container_name or instance.name,
+            port=tool_type.default_port,
+        )
+        instance.tunnel_id = tunnel_info["pid"]
+        instance.public_url = tunnel_info["url"]
+        instance.url = tunnel_info["url"]
+        logger.info(
+            "Created tunnel for instance %s: %s", instance.id, tunnel_info["url"]
+        )
+    except Exception as exc:
+        logger.error("Failed to create tunnel for instance %s: %s", instance.id, exc)
+        instance.status = "error"
+        instance.url = None
+
+
+async def _run_readiness_probe(
+    instance: ToolInstance, tool_type: ToolType
+) -> tuple[bool, list[str]]:
+    """Run readiness probe if configured."""
+    if not tool_type.readiness_probe or not instance.container_id:
+        return True, []
+
+    probe = tool_type.readiness_probe
+    command = probe.get("command", "")
+    if not command:
+        return True, []
+
+    return await execute_probe(
+        container_id=instance.container_id,
+        command=command,
+        timeout=probe.get("timeout", 30),
+        interval=probe.get("interval", 2),
+    )

apps/api/src/services/lifecycle_hooks.py

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

apps/api/src/services/manifest_compiler.py

@@ -8,6 +8,8 @@ from typing import Any
 
 import yaml
 
+from src.services.docker import sort_volumes_by_specificity
+
 
 def resolve_base(manifest: dict) -> dict:
     """Merge a base definition into a tool manifest.
@@ -24,7 +26,7 @@ def resolve_base(manifest: dict) -> dict:
     result = deepcopy(manifest)
 
     base_definition_id = result.pop("base_definition_id", None)
-    base_version = result.pop("base_version", "latest")
+    result.pop("base_version", None)
 
     if base_definition_id:
         # This will be provided by the caller (they have the DB session)
@@ -116,11 +118,16 @@ def compile_dockerfile(manifest: dict) -> str:
 
     # System packages (apt)
     apt_packages = manifest.get("packages", {}).get("apt", [])
+    if manifest.get("user"):
+        # Ensure sudo is available for permission-fixing startup scripts
+        apt_packages = list(apt_packages)
+        if "sudo" not in apt_packages:
+            apt_packages.append("sudo")
     if apt_packages:
-        lines.append("RUN apt-get update && apt-get install -y \\\\")
+        lines.append("RUN apt-get update && apt-get install -y \\")
         for pkg in apt_packages[:-1]:
-            lines.append(f"    {pkg} \\\\")
-        lines.append(f"    {apt_packages[-1]} \\\\")
+            lines.append(f"    {pkg} \\")
+        lines.append(f"    {apt_packages[-1]} \\")
         lines.append("    && rm -rf /var/lib/apt/lists/*")
         lines.append("")
 
@@ -129,9 +136,9 @@ def compile_dockerfile(manifest: dict) -> str:
     if node:
         version = node.get("version", "20")
         lines.append(
-            f"RUN curl -fsSL https://deb.nodesource.com/setup_{version}.x | bash - && \\\\"
+            f"RUN curl -fsSL https://deb.nodesource.com/setup_{version}.x | bash - && \\"
         )
-        lines.append("    apt-get install -y nodejs && \\\\")
+        lines.append("    apt-get install -y nodejs && \\")
         lines.append("    rm -rf /var/lib/apt/lists/*")
         lines.append("")
 
@@ -157,9 +164,25 @@ def compile_dockerfile(manifest: dict) -> str:
         gid = user["gid"]
         create_home = "-m " if user.get("create_home", True) else ""
         shell = user.get("shell", "/bin/bash")
-        lines.append(f"RUN groupadd -g {gid} {name} && \\\\")
+        lines.append(f"RUN groupadd -g {gid} {name} && \\")
         lines.append(f"    useradd -u {uid} -g {gid} {create_home}-s {shell} {name}")
         lines.append("")
+        # Set HOME and USER for runtime compatibility
+        home = f"/home/{name}"
+        lines.append(f"ENV HOME={home}")
+        lines.append(f"ENV USER={name}")
+        lines.append("")
+        # Ensure home directory exists and is writable by the user
+        lines.append(
+            f"RUN mkdir -p {home} && chown {name}:{name} {home} && chmod 755 {home}"
+        )
+        lines.append("")
+
+        # Configure passwordless sudo so startup scripts can fix permissions
+        lines.append(
+            f'RUN echo "{name} ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/{name} && chmod 0440 /etc/sudoers.d/{name}'
+        )
+        lines.append("")
 
     # Build scripts
     build_scripts = manifest.get("scripts", {}).get("build", [])
@@ -174,6 +197,11 @@ def compile_dockerfile(manifest: dict) -> str:
     if build_scripts:
         lines.append("")
 
+    # After build scripts, ensure everything in home is owned by the user
+    if user and build_scripts:
+        lines.append(f"RUN chown -R {name}:{name} {home}")
+        lines.append("")
+
     # Create mount target directories
     mounts = manifest.get("mounts", [])
     if mounts:
@@ -298,10 +326,24 @@ def compile_compose(manifest: dict, variables: dict[str, Any]) -> str:
         volumes.append(vol_str)
 
     if volumes:
-        service["volumes"] = volumes
+        service["volumes"] = sort_volumes_by_specificity(volumes)
 
     compose = {"services": {"app": service}}
-    return yaml.dump(compose, default_flow_style=False)
+    result = yaml.dump(compose, default_flow_style=False)
+
+    # Debug: log mount resolution so we can diagnose missing mounts
+    import logging
+    logger = logging.getLogger(__name__)
+    logger.debug(
+        "compile_compose: REPO_PATH=%s SSH_PATH=%s EXTRA_VOLUMES=%s mounts=%s volumes=%s",
+        variables.get("REPO_PATH", "<empty>"),
+        variables.get("SSH_PATH", "<empty>"),
+        variables.get("EXTRA_VOLUMES", []),
+        manifest.get("mounts", []),
+        volumes,
+    )
+
+    return result
 
 
 def resolve_mount_source(mount: dict, variables: dict[str, Any]) -> str:
@@ -333,6 +375,21 @@ def resolve_mount_source(mount: dict, variables: dict[str, Any]) -> str:
     return ""
 
 
+def get_manifest_home_dir(manifest: dict) -> str:
+    """Get the home directory for a container based on manifest user config.
+
+    Args:
+        manifest: Fully resolved manifest JSON.
+
+    Returns:
+        Home directory path (e.g., /home/user or /root).
+    """
+    user = manifest.get("user")
+    if user and user.get("name"):
+        return f"/home/{user['name']}"
+    return "/root"
+
+
 def compute_image_tag(tool_name: str, manifest: dict) -> str:
     """Compute a deterministic image tag from manifest content.
 
@@ -350,14 +407,11 @@ def compute_image_tag(tool_name: str, manifest: dict) -> str:
     return f"headquarter/{safe_name}-{hash_suffix}:latest"
 
 
-def merge_with_config(
-    manifest: dict, tool_configs: list[dict], profile: dict | None = None
-) -> dict:
-    """Merge ToolConfig and ConfigProfile overrides into a manifest.
+def merge_with_config(manifest: dict, profile: dict | None = None) -> dict:
+    """Merge ConfigProfile overrides into a manifest.
 
     Args:
         manifest: Base manifest from tool definition.
-        tool_configs: List of ToolConfig records.
         profile: Resolved ConfigProfile (optional).
 
     Returns:
@@ -365,29 +419,9 @@ def merge_with_config(
     """
     result = deepcopy(manifest)
 
-    # Apply ToolConfigs
     extra_env: dict[str, str] = {}
     extra_volumes: list[dict] = []
 
-    for config in tool_configs:
-        if config.get("config_type") == "env":
-            extra_env[config["key"]] = config["value"]
-        elif config.get("config_type") == "file" and config.get("file_path"):
-            # Files are handled outside the manifest (written to instance dir)
-            pass
-        if config.get("port_override"):
-            result["default_port"] = config["port_override"]
-        if config.get("start_command"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["command"] = config["start_command"].split()
-        if config.get("working_directory"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["working_dir"] = config["working_directory"]
-        if config.get("environment_variables"):
-            extra_env.update(config["environment_variables"])
-        if config.get("volumes"):
-            extra_volumes.extend(config["volumes"])
-
     # Apply ConfigProfile
     if profile:
         if profile.get("environment_variables"):

apps/api/src/services/notification_service.py

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

apps/api/src/services/permission_fixer.py

@@ -40,6 +40,17 @@ def apply_mount_permissions(
             "error": None,
         }
 
+        # Skip read-only mounts — their permissions cannot be changed
+        # post-start because the bind mount is locked.
+        if mount.get("readonly", False):
+            logger.debug(
+                "Skipping permission fix for read-only mount %s (target=%s)",
+                name,
+                target,
+            )
+            results.append(result)
+            continue
+
         # Skip if no permission policy defined
         if not owner and not mode and not file_mode:
             results.append(result)
@@ -104,6 +115,141 @@ def apply_mount_permissions(
     return results
 
 
+def _exec_and_log(
+    container_id: str,
+    command: list[str],
+    timeout: int,
+    description: str,
+) -> str:
+    """Run a docker exec command and log stdout/stderr for debugging."""
+    cmd = ["docker", "exec", "--user", "root", container_id] + command
+    logger.debug("[SSH-fix] %s: %s", description, " ".join(cmd))
+
+    try:
+        result = subprocess.run(
+            cmd,
+            capture_output=True,
+            text=True,
+            timeout=timeout,
+        )
+    except subprocess.TimeoutExpired:
+        raise PermissionFixError(
+            f"Command timed out after {timeout}s: {' '.join(command)}"
+        )
+    except FileNotFoundError:
+        raise PermissionFixError(f"Docker command not found: {' '.join(command)}")
+
+    stdout = result.stdout.strip()
+    stderr = result.stderr.strip()
+    if stdout:
+        logger.debug("[SSH-fix] %s stdout: %s", description, stdout)
+    if stderr:
+        logger.debug("[SSH-fix] %s stderr: %s", description, stderr)
+
+    if result.returncode != 0:
+        raise PermissionFixError(
+            f"Command failed (rc={result.returncode}): {stderr or '(no stderr)'}"
+        )
+    return stdout
+
+
+def apply_ssh_permissions(
+    container_id: str,
+    ssh_target: str,
+    container_user: str,
+    timeout: int = 10,
+) -> dict[str, Any]:
+    """Fix SSH directory ownership and permissions in a running container.
+
+    Runs chown and chmod on the ~/.ssh directory so the container user
+    can use the keys (SSH requires the private key to be owned by the
+    user with mode 600).
+
+    Args:
+        container_id: Docker container ID or name.
+        ssh_target: Absolute path to the .ssh directory inside the container.
+        container_user: The container user that should own the keys.
+        timeout: Max seconds per docker exec command.
+
+    Returns:
+        Result dict with keys: success, error.
+    """
+    result: dict[str, Any] = {"success": True, "error": None}
+    try:
+        # 1. Ensure directory is owned by the container user
+        _exec_and_log(
+            container_id,
+            ["chown", "-R", f"{container_user}:{container_user}", ssh_target],
+            timeout,
+            "chown",
+        )
+
+        # 2. Set directory permissions
+        _exec_and_log(
+            container_id,
+            ["chmod", "700", ssh_target],
+            timeout,
+            "chmod-dir",
+        )
+
+        # 3. Set private key permissions (id_ed25519, id_rsa, etc.)
+        _exec_and_log(
+            container_id,
+            [
+                "sh",
+                "-c",
+                f"find {ssh_target} -name 'id_*' -type f -exec chmod 600 {{}} +",
+            ],
+            timeout,
+            "chmod-keys",
+        )
+
+        # 4. Verify final state
+        ls_output = _exec_and_log(
+            container_id,
+            ["ls", "-la", ssh_target],
+            timeout,
+            "verify-ls",
+        )
+        stat_output = _exec_and_log(
+            container_id,
+            ["stat", "-c", "%U:%G %a %n", ssh_target],
+            timeout,
+            "verify-stat-dir",
+        )
+        key_stat = _exec_and_log(
+            container_id,
+            [
+                "sh",
+                "-c",
+                f"stat -c '%U:%G %a %n' {ssh_target}/id_* 2>/dev/null || echo 'no id_* files found'",
+            ],
+            timeout,
+            "verify-stat-keys",
+        )
+
+        logger.info(
+            "SSH permissions fixed for container %s (user=%s, target=%s). "
+            "ls:\n%s\nstat-dir: %s\nstat-keys: %s",
+            container_id,
+            container_user,
+            ssh_target,
+            ls_output,
+            stat_output,
+            key_stat,
+        )
+    except PermissionFixError as exc:
+        result["success"] = False
+        result["error"] = str(exc)
+        logger.warning(
+            "SSH permission fix failed for container %s (target=%s): %s",
+            container_id,
+            ssh_target,
+            exc,
+        )
+    return result
+
+
 class PermissionFixError(Exception):
     """Raised when a permission fix command fails."""
 

apps/api/src/services/profile_resolver.py

@@ -0,0 +1,251 @@
+"""Profile resolver service for recursive ordered include resolution.
+
+Provides deterministic merge rules, save-independent cycle protection,
+and resolved output structures for env vars, runtime hints, mounts,
+file trees, and override metadata.
+"""
+
+from __future__ import annotations
+
+import uuid
+from dataclasses import dataclass, field
+
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
+
+
+@dataclass
+class ResolvedMount:
+    """A resolved mount with merged file tree and final mode."""
+
+    target_path: str
+    mode: str  # "ro" or "rw"
+    files: dict[str, str] = field(default_factory=dict)
+    """Relative file paths to UTF-8 text content."""
+    overridden_files: dict[str, list[str]] = field(default_factory=dict)
+    """Map of relative file path to list of profile names that contributed
+    (latest is the winner)."""
+    mode_overridden_by: str | None = None
+    """Name of the profile that set the final mode, if different from first."""
+
+
+@dataclass
+class ResolvedRuntimeHints:
+    """Resolved runtime hints from profile layers."""
+
+    start_command: str | None = None
+    working_directory: str | None = None
+    port: int | None = None
+    overridden_hints: dict[str, str] = field(default_factory=dict)
+    """Map of hint key to profile name that provided the winning value."""
+
+
+@dataclass
+class ResolvedProfileOutput:
+    """Complete resolved output for a config profile."""
+
+    profile_id: uuid.UUID
+    profile_name: str
+    environment_variables: dict[str, str] = field(default_factory=dict)
+    """Final merged env vars (later layers win)."""
+    env_var_sources: dict[str, list[str]] = field(default_factory=dict)
+    """Map of env var key to ordered list of contributing profile names
+    (latest is the winner)."""
+    runtime_hints: ResolvedRuntimeHints = field(
+        default_factory=lambda: ResolvedRuntimeHints()
+    )
+    mounts: dict[str, ResolvedMount] = field(default_factory=dict)
+    """Map of target_path to ResolvedMount."""
+    resolution_order: list[str] = field(default_factory=list)
+    """Ordered list of profile names as they were resolved."""
+    cycle_detected: bool = False
+    cycle_path: list[str] | None = None
+
+
+class ProfileResolutionError(Exception):
+    """Raised when profile resolution fails."""
+
+    pass
+
+
+class ProfileCycleError(ProfileResolutionError):
+    """Raised when a cycle is detected during profile resolution."""
+
+    def __init__(self, cycle_path: list[str]) -> None:
+        self.cycle_path = cycle_path
+        path_str = " -> ".join(cycle_path)
+        super().__init__(f"Profile include cycle detected: {path_str}")
+
+
+def _merge_env_vars(
+    current: dict[str, str],
+    sources: dict[str, list[str]],
+    profile: ConfigProfile,
+) -> None:
+    """Merge a profile's env vars into the current dict, tracking sources."""
+    if not profile.environment_variables:
+        return
+    for key, value in profile.environment_variables.items():
+        current[key] = value
+        if key not in sources:
+            sources[key] = []
+        sources[key].append(profile.name)
+
+
+def _merge_runtime_hints(
+    hints: ResolvedRuntimeHints,
+    profile: ConfigProfile,
+) -> None:
+    """Merge a profile's runtime hints, tracking overrides."""
+    if profile.start_command is not None:
+        hints.start_command = profile.start_command
+        hints.overridden_hints["start_command"] = profile.name
+    if profile.working_directory is not None:
+        hints.working_directory = profile.working_directory
+        hints.overridden_hints["working_directory"] = profile.name
+    if profile.port is not None:
+        hints.port = profile.port
+        hints.overridden_hints["port"] = profile.name
+
+
+def _merge_mounts(
+    mounts: dict[str, ResolvedMount],
+    profile_mounts: list[ConfigMount],
+    profile: ConfigProfile,
+) -> None:
+    """Merge a profile's mounts into the current mounts dict."""
+    for mount in profile_mounts:
+        target = mount.target_path
+        if target not in mounts:
+            mounts[target] = ResolvedMount(
+                target_path=target,
+                mode=mount.mode,
+                files={},
+                overridden_files={},
+            )
+        resolved = mounts[target]
+        
+        # Mode override: later wins
+        if resolved.mode != mount.mode:
+            resolved.mode = mount.mode
+            resolved.mode_overridden_by = profile.name
+        
+        # File tree merge: later wins for same relative path
+        if mount.files:
+            for rel_path, content in mount.files.items():
+                if rel_path not in resolved.files:
+                    resolved.overridden_files[rel_path] = []
+                else:
+                    if rel_path not in resolved.overridden_files:
+                        resolved.overridden_files[rel_path] = []
+                    resolved.overridden_files[rel_path].append(profile.name)
+                resolved.files[rel_path] = content
+
+
+def _resolve_profile_recursive(
+    profile: ConfigProfile,
+    visited: set[uuid.UUID],
+    path: list[str],
+    resolution_order: list[str],
+    env_vars: dict[str, str],
+    env_var_sources: dict[str, list[str]],
+    runtime_hints: ResolvedRuntimeHints,
+    mounts: dict[str, ResolvedMount],
+) -> None:
+    """Recursively resolve a profile and its includes.
+
+    Args:
+        profile: The profile to resolve
+        visited: Set of already-resolved profile IDs to avoid duplicates
+        path: Current recursion path for cycle detection
+        resolution_order: Ordered list of profile names being resolved
+        env_vars: Accumulated environment variables
+        env_var_sources: Tracking of which profiles contributed each env var
+        runtime_hints: Accumulated runtime hints
+        mounts: Accumulated mounts
+
+    Raises:
+        ProfileCycleError: If a cycle is detected
+    """
+    if profile.name in path:
+        # Cycle detected
+        cycle_start = path.index(profile.name)
+        cycle_path = path[cycle_start:] + [profile.name]
+        raise ProfileCycleError(cycle_path)
+
+    if profile.id in visited:
+        # Already resolved in another branch (diamond graph)
+        return
+
+    visited.add(profile.id)
+    path.append(profile.name)
+    resolution_order.append(profile.name)
+
+    # Resolve includes first (in order)
+    includes: list[ConfigInclude] = list(profile.includes)
+    includes.sort(key=lambda inc: inc.order_index)
+    for include in includes:
+        included_profile = include.included_profile
+        if included_profile is not None:
+            _resolve_profile_recursive(
+                included_profile,
+                visited,
+                path,
+                resolution_order,
+                env_vars,
+                env_var_sources,
+                runtime_hints,
+                mounts,
+            )
+
+    # Apply this profile's values (later layers win)
+    _merge_env_vars(env_vars, env_var_sources, profile)
+    _merge_runtime_hints(runtime_hints, profile)
+    _merge_mounts(mounts, list(profile.mounts), profile)
+
+    path.pop()
+
+
+def resolve_profile(profile: ConfigProfile) -> ResolvedProfileOutput:
+    """Resolve a config profile with all its includes.
+
+    Processes included profiles in configured order, then applies the
+    selected profile itself. Later layers override earlier layers.
+
+    Args:
+        profile: The root profile to resolve
+
+    Returns:
+        ResolvedProfileOutput with merged env vars, runtime hints, mounts,
+        and override metadata
+
+    Raises:
+        ProfileCycleError: If a cycle is detected in the include graph
+    """
+    env_vars: dict[str, str] = {}
+    env_var_sources: dict[str, list[str]] = {}
+    runtime_hints = ResolvedRuntimeHints()
+    mounts: dict[str, ResolvedMount] = {}
+    resolution_order: list[str] = []
+
+    _resolve_profile_recursive(
+        profile,
+        set(),
+        [],
+        resolution_order,
+        env_vars,
+        env_var_sources,
+        runtime_hints,
+        mounts,
+    )
+
+    return ResolvedProfileOutput(
+        profile_id=profile.id,
+        profile_name=profile.name,
+        environment_variables=env_vars,
+        env_var_sources=env_var_sources,
+        runtime_hints=runtime_hints,
+        mounts=mounts,
+        resolution_order=resolution_order,
+    )

apps/api/src/services/ssh_keys.py

@@ -1,12 +1,16 @@
 """SSH key service utilities for preparing keys for container use."""
 
+import logging
 import os
+import re
 from pathlib import Path
 
 from cryptography.fernet import Fernet
 
 from src.config import Settings
 
+logger = logging.getLogger(__name__)
+
 
 def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
@@ -19,17 +23,48 @@ def _get_fernet() -> Fernet:
     return Fernet(key)
 
 
-def prepare_ssh_key_files(instance_dir: str, ssh_key) -> str:
+def _sanitize_filename(name: str) -> str:
+    """Sanitize a string for use as a filename.
+
+    Replaces non-alphanumeric characters with underscores and strips
+    leading/trailing underscores.
+    """
+    sanitized = re.sub(r"[^a-zA-Z0-9_-]", "_", name)
+    sanitized = sanitized.strip("_")
+    # Ensure it's not empty
+    if not sanitized:
+        sanitized = "key"
+    return sanitized
+
+
+def prepare_ssh_key_files(
+    instance_dir: str,
+    ssh_key,
+    subdir: str = ".ssh",
+    uid: int | None = None,
+    gid: int | None = None,
+    key_filename: str = "id_ed25519",
+    write_config: bool = True,
+) -> str:
     """Decrypt and write SSH key files to instance directory for container mounting.
 
     Args:
         instance_dir: Path to instance directory
         ssh_key: SSHKey model instance with encrypted private key
+        subdir: Subdirectory within instance_dir to write to (default: ".ssh")
+        uid: Optional UID to own the files (for bind-mount into non-root container)
+        gid: Optional GID to own the files
+        key_filename: Base filename for the key pair (default: "id_ed25519").
+            The private key will be named "{key_filename}" and the public key
+            "{key_filename}.pub".
+        write_config: Whether to write an SSH config file (default: True).
+            Set to False when combining multiple keys into one directory,
+            then call write_ssh_config() separately.
 
     Returns:
         Path to the .ssh directory
     """
-    ssh_dir = Path(instance_dir) / ".ssh"
+    ssh_dir = Path(instance_dir) / subdir
     ssh_dir.mkdir(parents=True, exist_ok=True)
 
     # Decrypt private key
@@ -37,27 +72,101 @@ def prepare_ssh_key_files(instance_dir: str, ssh_key) -> str:
     private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
 
     # Write private key with restricted permissions
-    private_key_path = ssh_dir / "id_ed25519"
+    private_key_path = ssh_dir / key_filename
     private_key_path.write_text(private_key)
     os.chmod(private_key_path, 0o600)
 
     # Write public key
-    public_key_path = ssh_dir / "id_ed25519.pub"
+    public_key_path = ssh_dir / f"{key_filename}.pub"
     public_key_path.write_text(ssh_key.public_key)
     os.chmod(public_key_path, 0o644)
 
-    # Write SSH config
-    config_path = ssh_dir / "config"
-    config_content = """Host *
+    # Write SSH config (only if requested)
+    if write_config:
+        config_path = ssh_dir / "config"
+        config_content = f"""Host *
     StrictHostKeyChecking no
     UserKnownHostsFile /dev/null
-    IdentityFile ~/.ssh/id_ed25519
+    IdentityFile ~/.ssh/{key_filename}
     IdentitiesOnly yes
 """
+        config_path.write_text(config_content)
+        os.chmod(config_path, 0o644)
+
+        # Set ownership to target container user if requested
+        if uid is not None or gid is not None:
+            effective_uid = uid if uid is not None else -1
+            effective_gid = gid if gid is not None else -1
+            try:
+                os.chown(ssh_dir, effective_uid, effective_gid)
+                os.chown(private_key_path, effective_uid, effective_gid)
+                os.chown(public_key_path, effective_uid, effective_gid)
+                os.chown(config_path, effective_uid, effective_gid)
+                logger.debug(
+                    "Set SSH key ownership to uid=%s gid=%s for %s",
+                    effective_uid,
+                    effective_gid,
+                    ssh_dir,
+                )
+            except PermissionError as exc:
+                logger.warning(
+                    "Cannot chown SSH keys to uid=%s gid=%s (running as uid=%s): %s",
+                    effective_uid,
+                    effective_gid,
+                    os.getuid(),
+                    exc,
+                )
+    else:
+        # Still chown the key files even if we didn't write config
+        if uid is not None or gid is not None:
+            effective_uid = uid if uid is not None else -1
+            effective_gid = gid if gid is not None else -1
+            try:
+                os.chown(private_key_path, effective_uid, effective_gid)
+                os.chown(public_key_path, effective_uid, effective_gid)
+            except PermissionError:
+                pass
+
+    return str(ssh_dir)
+
+
+def write_ssh_config(
+    ssh_dir: str,
+    key_filenames: list[str],
+    uid: int | None = None,
+    gid: int | None = None,
+) -> None:
+    """Write an SSH config file that includes multiple IdentityFile entries.
+
+    Args:
+        ssh_dir: Path to the .ssh directory
+        key_filenames: List of key filenames (without .pub extension)
+        uid: Optional UID to own the config file
+        gid: Optional GID to own the config file
+    """
+    ssh_dir_path = Path(ssh_dir)
+    ssh_dir_path.mkdir(parents=True, exist_ok=True)
+
+    config_path = ssh_dir_path / "config"
+    lines = ["Host *"]
+    lines.append("    StrictHostKeyChecking no")
+    lines.append("    UserKnownHostsFile /dev/null")
+    lines.append("    IdentitiesOnly yes")
+    for filename in key_filenames:
+        lines.append(f"    IdentityFile ~/.ssh/{filename}")
+    lines.append("")
+
+    config_content = "\n".join(lines)
     config_path.write_text(config_content)
     os.chmod(config_path, 0o644)
 
-    return str(ssh_dir)
+    if uid is not None or gid is not None:
+        effective_uid = uid if uid is not None else -1
+        effective_gid = gid if gid is not None else -1
+        try:
+            os.chown(config_path, effective_uid, effective_gid)
+        except PermissionError:
+            pass
 
 
 def cleanup_ssh_key_files(instance_dir: str) -> None: