Unify in-memory session state in AgentSessionOrchestrator ...

Replace scattered _runs + _busy_sessions + _session_sockets with a
single _sessions: dict[str, SessionState] on the orchestrator.

- SessionState dataclass holds run, busy_event, and websockets
- _session_sockets module-level global removed from websocket.py;
  socket tracking moved into orchestrator (add/remove_websocket)
- Event bus subscriber _on_recall_update moved into orchestrator
- Per-session asyncio.Lock added to protect concurrent-run guard
- _cleanup() auto-removes empty SessionState entries

Tests updated to reference _sessions instead of legacy _runs.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Extract single shared Database pool, eliminate 4 duplicated pool creations ...

- Create navi/db.py::Database managing one asyncpg pool
- KvStore, PgSessionStore, MemoryStore, RecallScheduler now accept pool in constructor
- AppContainer holds Database, shutdown closes one pool instead of 4
- create_container creates one pool and passes it to all stores
- All tests updated to set _initialized=True on fakes to skip DDL

392 passed, 1 skipped

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Make Settings immutable (frozen=True) and fix all test mutations ...

- Add frozen=True to SettingsConfigDict in navi/config.py
- Convert model_validator to mode="before" since mode="after" cannot mutate frozen instances
- Replace all field-level monkeypatches in tests with whole-Settings object replacement
- Ensure cross-module settings consistency (content_store, session_files, share_file, content_publish, filesystem)

392 passed, 1 skipped

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Extract WebSocket business logic into AgentSessionOrchestrator ...

- Create navi/core/orchestrator.py with AgentSessionOrchestrator and SessionRun
- Orchestrator owns _runs, _busy_sessions, Agent creation, run_agent(), run_recall()
- Transport-agnostic: accepts notify callback from WebSocket handler
- WebSocket handler (websocket.py) now only does serialization/deserialization
- _fire_recall delegates to orchestrator.run_recall() instead of inline logic
- recall_scheduler_loop now accepts orchestrator parameter
- AppContainer gains .orchestrator field, created in create_container()
- deps.py: add get_orchestrator()
- Update integration tests for scheduler_loop and websocket unit tests

All 392 tests pass.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Replace global lazy singletons with explicit AppContainer + lifespan ...

- Create navi/core/container.py with AppContainer dataclass and create_container()
- Rewrite navi/api/deps.py: remove module-level singletons, add _container global
  fallback + set_container(), use _resolve_container() for all getters
- Replace @app.on_event with @asynccontextmanager lifespan in main.py
- Update routes to use Depends(get_scheduler) instead of calling get_scheduler()
- Fix FastAPI body parsing bug: remove dataclass parameters from Depends getters
  (FastAPI was treating AppContainer sub-dependencies as Body params, forcing
  embed=True on all endpoint body params and causing 422 errors)
- Update websocket.py to use _resolve_container() instead of get_registries()
- Update integration test fixtures to build AppContainer and call set_container()
- Remove obsolete tests/unit/test_startup.py (tests removed _on_startup)
- Fix test_scheduler_loop.py fixture (get_registries no longer exists)

All 387 tests pass (excluding websocket hang tests).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

fix(recall): stabilize scheduled callback system and improve UX ...

Backend fixes:
- stop_session now stops headless recall runs via _busy_sessions dict
- _fire_recall sets user ContextVars so tools work correctly
- MaxIterationsReached treated as success, not failure
- skip_next_recall uses GREATEST(trigger_at, now) for overdue recalls
- schedule_recall rejects past trigger times
- timezone offset double-adjustment fixed for aware datetimes
- _fire_recall registers _AgentRun for reconnect/replay support
- session_sync race with stream_start fixed

Frontend improvements:
- Recall banner moved to ChatHeader with live Cancel/Skip buttons
- Recall messages styled with is_recall flag and badge
- Real-time recall updates via WebSocket (recall_update events)
- Recall filter moved to sessions-header as toggle button
- Session list shows clock icon for sessions with pending recall
- Empty state messages for empty/filtered session lists
- Fixed missing api import in ChatHeader.vue

Tests:
- Updated scheduler_loop tests for _busy_sessions dict change

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Add self-recall (scheduled callback) system ...

Core features:
- schedule_recall tool: once/recurring/immediate callbacks
- manage_recall tool: cancel/skip/list scheduled recalls
- Natural-language time parser (ISO, relative, "tomorrow at 09:00")
- PostgreSQL-backed RecallScheduler with lazy pool init
- Background recall_scheduler_loop with asyncio.Semaphore(3)
- _busy_sessions guard prevents user messages during headless runs
- Agent.run() preserves thinking field for session history visibility
- API endpoints: GET/DELETE/POST for session recall, admin list
- Frontend: recall badge, filter, cancel/skip in sidebar and chat header
- Tests: parser, scheduler CRUD, tools, API, scheduler loop (53 tests)
- Manuals: schedule_recall.md and manage_recall.md

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Fix MCP tool lookup in websocket handler and tests ...

- websocket.py: pass mcp_manager to Agent(), with graceful fallback
  if MCP connection fails
- conftest.py: mock get_mcp_manager() in tests to prevent SSE
  connection attempts against real servers

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Add MCP server support and fix memory tools user isolation ...

MCP integration:
- New navi/mcp/ package: client, manager, config, tools
- ToolRegistry learns register_external() for MCP tools
- reload_tools reconnects MCP servers on hot reload
- New built-in mcp_status tool
- Startup/shutdown wiring for MCP connections
- 12 new tests (unit + integration with real stdio server)

Memory tools fix:
- memory, memory_save, memory_search, memory_forget now read
  current_user_id from tool context and pass it to MemoryStore
- Fixes invisible facts for authenticated users

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Add pagination, search, and sorting to admin sessions ...

Backend:
- Add count_all and search_list abstract methods to SessionStore
- Implement count_all and search_list in PgSessionStore (SQL with ILIKE)
- Implement count_all and search_list in InMemorySessionStore
- Update /admin/sessions to accept limit, offset, search, sort_by, sort_order
- Return {total, limit, offset, items} from /admin/sessions

Frontend:
- Add search input for sessions in admin panel
- Add clickable sortable column headers with asc/desc toggle
- Add pagination controls (prev/next, page size selector, item count)
- Debounce search input (300ms)

Tests:
- Add integration tests for pagination, offset, search, and sorting
- All 217 tests pass

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Fix WebSocket 403 — bypass FastAPI Depends for WS auth ...

- websocket.py: resolve user by calling get_current_user_ws directly
  inside the handler instead of using Depends(). This avoids FastAPI
  returning HTTP 403 on the upgrade request when auth resolution fails.
- websocket.py: accept WebSocket before access check, close with 4003
  for auth failures instead of HTTP 403.
- auth/deps.py: remove debug logging from get_current_user_ws.
- tests/conftest.py: monkeypatch get_current_user_ws directly since
  Depends() is no longer used on the WebSocket endpoint.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Multi-user auth via gnexus-auth OAuth + hybrid role/permission model ...

- Integrate gnexus-auth-client-py (GAuthClient) for OAuth flow, token refresh,
  and webhook parsing
- Add navi/auth/ package: User model, Fernet encryptor, client singleton,
  deps (get_current_user, require_admin, require_permission)
- New tables: navi_users, user_auth_sessions (auto-created on startup)
- Session/memory isolation by user_id with legacy NULL support
- Cookie-based auth proxy: /auth/login, /callback, /logout, /me
- Webhook receiver /webhooks/gnexus-auth handling user events, global logout,
  session revocation, role/permission changes
- Admin endpoints (/admin/*) gated by role + permissions
- Webclient auth store with isAdmin/hasPermission guards
- Admin-only profile filtering in /agents/profiles
- 200/200 tests passing

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Paginate session list loading

Add 62 tests across all planned phases + fix integration flakiness ...

- Phase 3: 19 API route integration tests (health, agents, sessions, messages)
- Phase 3: 7 WebSocket integration tests (connect, send, replay, invalid, stop)
- Phase 4: 9 agent tests (_check_context_size, _iter_stream_guarded)
- Phase 4: 5 planning tests (_parse_plan_steps)
- Phase 5: 22 tool tests (filesystem 13, code_exec 5, terminal 4)
- Fix flaky integration tests by patching module-level singletons
  (_session_store, _registries, _workers) instead of getter functions,
  because FastAPI Depends() captures the original function at import time.
- Update docs/testing.md coverage table (150 total tests)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>