McpTool: auto-inject session_id + normalize navi-3d paths ...

- McpTool.execute() now forces the real session_id from current_session_id
  ContextVar, preventing LLM hallucinations of wrong UUIDs (ghost-session bug).
- For navi-3d MCP server, source_path/output_path are normalized to basename
  to prevent double path nesting when the LLM passes full relative paths.
- Updated MCP tool descriptions to ask for filenames only.
- Added system prompt instructions in context_builder and subagent_runner
  reminding the model to pass bare filenames to navi-3d tools.

396 passed, 1 skipped

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>

Add WebSocket handler unit tests ...

Tests for reconnect/replay, concurrent-run guard, event buffering,
and session_sync behavior after both normal and recall runs.

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 session file URLs (add /api prefix) and WebGL error handling in STL viewer ...

Backend:
- _file_url in content_store.py now returns /api/sessions/... instead of /sessions/...
- share_file.py URL construction updated to include /api
- content_publish.py docstring updated to reflect correct endpoint

Frontend:
- contentLinks.js: avoid double /api prefix in dev mode when backend already returns it
- stl.html: replace throw err with return after showing WebGL fallback message
- Rebuild dist

Tests:
- Update expected URLs in test_content_store.py and test_share_file.py

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

Step 4: Extract SubAgentRunner from run_ephemeral() ...

- Create navi/core/subagent_runner.py with full sub-agent loop logic
- Move _iter_stream_guarded to navi/core/stream_guard.py
- Move _check_context_size to ContextCompressor.check_context_size()
- Extract build_tool_list() and load_user_enabled_tools() to tool_utils.py
- Agent.run_ephemeral() becomes a thin wrapper delegating to SubAgentRunner
- Remove ~310 lines from agent.py
- All existing run_ephemeral tests pass unchanged

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

Step 3: Extract AntiStallMonitor from run_stream() ...

- Create navi/core/anti_stall.py with AntiStallMonitor class
- Encapsulates stall detection (todo progress + repeated tool calls)
- Encapsulates adaptive re-plan (failed todo step detection)
- Provides init() / pre_turn() / post_turn() two-phase interface
- Remove ~50 lines of stall/replan logic from agent.py run_stream()
- Remove _todo_status_snapshot and _todo_failed_steps helpers from agent.py
- Update AgentTurnContext: remove stall fields (now live in AntiStallMonitor)
- Add 13 unit tests for pre_turn and post_turn behavior

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

Extract ContextCompressor, fix STL viewer, expand test suite, add architecture audit docs ...

- Extract ContextCompressor from agent.py (Step 1 of god-object refactor)
- Add retry + hard-truncate fallback logic to ContextCompressor
- Add unit tests: agent loop (14), compressor (18), KV store (8),
  auth encrypt (3), auth deps (13), todo/scratchpad/image_view/memory
- Fix WebGL STL viewer: allow-same-origin sandbox + graceful fallback
- Add CompressionStarted event and client-side compression notice
- Add docs/architecture_weak_spots.md and plan_01_god_object_agent.md
- Update test_events.py and test_agent_context_size.py for new logic

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

Fix review issues: KV-store NULL, SVG messages, filesystem tests + docs ...

Bugs fixed:
- filesystem.py: add missing `import re` (grep was broken in production)
- image_view.py: consistent SVG rejection message for URL and file paths
- store/__init__.py: normalize user_id None→'' to prevent duplicate rows
  in unique constraint for anonymous sessions; add DDL migration for
  existing NULL values

Tests:
- Add 10 unit tests for filesystem copy, grep, diff operations

Documentation:
- agent.md: document streaming guard wrapper, system prompt caching,
  ContextVar restoration in subagents
- tools.md: document middleware hooks
- websocket.md: document image upload limits and concurrent run guard
- store.md: document user_id normalization
- mechanics.md: mark newly-documented mechanics as documented

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

Fix test_rejects_empty to match current _check_path behavior ...

Empty string is explicitly rejected by _check_path since the
guard clause was added. The test comment was stale.

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

Enhance native toolset and add persistent KV store ...

- Add PostgreSQL-backed KvStore (navi/store/) for session-scoped data.
- Migrate todo and scratchpad from in-memory dicts to KvStore.
- Filesystem: add copy, grep, diff actions; compress description.
- CodeExec: remove language param, expose working_dir in schema.
- ImageView: resize to 1024px JPEG + Content-Type guard for URLs.
- Memory list: return distinct categories instead of all facts.
- SSH: add scp action with upload/download support.
- Update CLAUDE.md (Postgres-only), docs/tools.md, add docs/store.md.
- Fix agent/planning/context_builder async signatures for todo helpers.

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>

Refactor: move tool helper modules into _internal subpackage ...

Moves non-tool infrastructure out of navi/tools/ root so that only
actual tool classes live there:

  base.py           → _internal/base.py
  loader.py         → _internal/loader.py
  middleware.py     → _internal/middleware.py
  logging_middleware.py → _internal/logging_middleware.py
  _time_parser.py   → _internal/time_parser.py

All imports updated across core/, api/, mcp/, tools/, and tests/.
No proxy files remain in navi/tools/ root.

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 gnexus-book MCP instructions and add old-format fallback in tool executor ...

- Updated mcp_servers.json gnexus-book instructions to use mcp:gnexus-book:
  prefix instead of the old mcp_gnexus-book_ format.
- Added fallback in tool_executor.py for old underscore format
  (mcp_server_tool → mcp:server:tool) so transitional models still work.
- Added unit test for the old-format fallback.

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

Rename MCP tools to mcp:server:tool format and restore human-readable names ...

- Core naming: mcp_server_tool → mcp:server:tool (colon-delimited)
- navi-web tools: search/view/request → web_search/web_view/http_request
- navi-3d tools: compile_scad/render_stl/lint_scad (unchanged names)
- Updated all profile configs, system prompts, docs, manuals, tests
- Added new lint_scad.md manual
- Fixed modeler_3d prompt stale references (scad_lint, model_3d, render_3d)
- All 240 tests pass

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

Migrate 3D modeling tools to standalone MCP server navi-3d ...

Phase 0 — Fix MCP error propagation:
- McpClient.call_tool now returns (output, is_error) tuple
- McpTool.execute sets success=False when MCP reports isError=True
- Fixes silent failures where MCP errors looked like success

Phase 1 — Create mcp-server-navi-3d:
- New standalone MCP server in mcp-servers/navi-3d/
- Tools: compile_scad, render_stl, lint_scad
- Session-scoped path resolution via SESSION_FILES_DIR env
- Anti-escape validation for security
- Includes tests/unit/test_scad_analyze.py

Phase 2 — Remove from Navi core:
- Deleted navi/tools/{model_3d,render_3d,scad_lint}.py
- Removed from registry.py builtins and navi/tools/__init__.py
- Updated pyproject.toml testpaths to exclude mcp-servers/

Phase 3 — Wire into Navi config:
- Added navi-3d block to mcp_servers.json (SSE on :8002)
- Updated modeler_3d profile: mcp_servers + updated system_prompt
- All old tool names replaced with mcp_navi-3d_* equivalents

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

Handle MCP tool aliases robustly

Clarify knowledge persistence prompts

Fix ollama_backends / FallbackOllamaBackend issues ...

- registry.py: always use FallbackOllamaBackend (unified backend).
  Enables model priority lists in all deployments, not just multi-server.
- agent.py: add missing think=profile.think_enabled to run() (REST endpoint).
- compressor.py: fix model param type (str → list[str] | str | None).
- fallback.py: harden load_servers_from_file against missing/bad JSON files
  and entries without host. Add clear_blacklists() for manual reset.
- admin.py: add POST /admin/ollama/clear-blacklists endpoint.
- tech_debt_review: document dead stream() methods.
- tests: add tests for single-server fallback, bad file handling,
  missing host skipping, and blacklist clearing.

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>

Fix admin memory showing 0 facts; add pagination/search/sort ...

Bug fix:
- get_all_facts(user_id=None) was filtering for user_id IS NULL only,
  so admin panel showed 0 facts when facts had user_ids set.
- Added all_users parameter to get_all_facts and fact_count.
- Admin endpoint now passes all_users=True to return all facts.

Memory pagination:
- Extended get_all_facts with offset, search, sort_by, sort_order params.
- Extended fact_count with search and all_users params.
- /admin/memory endpoint now accepts limit, offset, search, sort_by,
  sort_order and returns {total, limit, offset, items}.

Admin panel frontend:
- Added server-side search with debounce for memory facts.
- Added sortable column headers (category, key, source, confidence, updated).
- Added pagination controls (prev/next, page size selector).
- Switched memory display from grouped tables to flat sortable table.

Tests:
- Added unit tests for get_all_facts(all_users=True) and
  fact_count(all_users=True).
- All 219 tests pass.

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 memory system bugs: deterministic summary id, skip legacy extraction ...

- _summary.py: replace non-deterministic hash() with zlib.crc32 so
  summary id stays stable across server restarts, preventing duplicate
  summary rows.
- extractor.py: skip memory extraction for legacy sessions (user_id=None)
  — ON CONFLICT(user_id, category, key) does not catch NULL duplicates
  in PostgreSQL (NULL != NULL).
- sessions.py: _process_stale_sessions skips legacy sessions.
- _facts.py: remove dead code (user_clause/user_param variables).
- test_extractor.py: add user_id to test sessions + new test for
  legacy session skip.

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>

Allow subagents to use selected profiles