Fix MCP transport teardown race with anyio task groups

Apply review fixes to API token auth system ...

Backend:
- navi/auth/deps.py: replace 3 DB round-trips with single JOIN query for
  token resolution; update last_used_at still separate (best-effort)
- navi/api/routes/api_tokens.py: replace asyncpg-specific "UPDATE 1"
  string check with RETURNING id fetchrow; increase token_prefix from
  8 to 12 chars for better visual identification; add security notes
- tests/unit/auth/test_api_tokens.py: update tests for JOIN query and
  RETURNING-based revoke

Frontend:
- webclient/src/components/settings/ShowTokenModal.vue: new modal that
  shows the plain token in a readonly field with copy button and
  explicit warning — replaces the transient toast notification
- webclient/src/components/settings/ApiKeysPanel.vue: use ShowTokenModal
- webclient/src/composables/useWebSocket.js: add security comment about
  localStorage XSS risk and query param log exposure

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

Add API token auth system for headless/micro clients ...

Backend:
- navi/auth/_ddl.py: add api_tokens table with boot-time migration
- navi/auth/deps.py: _resolve_user now falls back to X-Api-Token header
  and ?api_token query param for WebSocket auth
- navi/auth/__init__.py: add ApiToken pydantic model
- navi/api/routes/api_tokens.py: CRUD endpoints (POST/GET/DELETE)
- navi/main.py: wire api_tokens router

Frontend:
- webclient/src/App.vue: add #settings hash routing
- webclient/src/components/settings/: SettingsView, ApiKeysPanel,
  CreateKeyModal with copy-to-clipboard flow
- webclient/src/api/index.js: token CRUD API functions
- webclient/src/stores/apiTokens.js: Pinia store
- webclient/src/components/sidebar/AppSidebar.vue: settings link
- webclient/src/composables/useWebSocket.js: append ?api_token= when
  localStorage token is present

Tests:
- tests/unit/auth/test_api_tokens.py: 10 unit tests covering token
  resolution (header + query param), revoke, missing/revoked tokens,
  orphan users, and CRUD endpoints

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

Enable gnexus-creds MCP in profiles that already use gnexus-book ...

- discuss: add gnexus-creds read group to agent tools
- server_admin: add gnexus-creds read+write groups to agent and subagent tools

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

Add MCP streamable_http transport, integrate gnexus-creds, and document headless nodes ...

- navi/mcp/client.py: add streamable_http transport via httpx + mcp.client.streamable_http
- navi/mcp/config.py: add "streamable_http" to transport literal and is_streamable_http property
- mcp_servers.d/gnexus-creds.json: new MCP server config with overlay instructions for secret workflow
- docs/future_headless_nodes.md: architecture exploration for headless Navi node swarm

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

Fix recall race, ContextVar leaks, dead code, and recall duplication ...

- run_recall: wrap busy check + create_run in session_lock to prevent
  race between scheduler and websocket handler
- run_recall: save ContextVar tokens and reset in finally to avoid
  leaking user context into subsequent background tasks
- websocket.py: reset user ContextVars in finally after run completes
- orchestrator.py: remove dead set_notify / _notify abstraction
- orchestrator.py: extract _finalize_recall to deduplicate success /
  MaxIterationsReached / Exception finalization blocks

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

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>

Pass explicit ToolContext to tools instead of hidden ContextVars ...

Add ToolContext dataclass (session_id, event_sink, stop_event, model,
user_id, user_role, user_info) and thread it through the execution chain:
Agent._execute_tools_with_sink → ToolExecutor → tool.execute().

All ~25 tools updated to accept ctx parameter. Tools that previously
read ContextVar now prefer ctx when provided, falling back to
ContextVar for backward compatibility.

Tests updated to pass ToolContext explicitly — no more test fixtures
that set current_session_id / current_user_id ContextVars.

ContextVar setters remain as fallback for non-tool consumers
(ai_helper, context_builder, planning) and will be removed in a
follow-up refactor.

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

Fix auth race condition causing frequent logouts ...

Add per-session-id asyncio.Lock around token refresh to prevent
parallel requests from simultaneously refreshing the same token.
Re-read the session inside the lock so a second request can use
the token already refreshed by the first one.

Stop deleting the auth session on refresh failure — transient
errors (network, race condition, expired refresh token) were
wiping the session and forcing a full re-login.

+ tests for both behaviours.

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

Prioritise gemma4 and add MCP tools to subagent scopes ...

- modeler_3d: gemma4:31b-cloud first (vision-capable), drop glm-5.1
- modeler_3d subagent: add navi-3d + navi-web MCP tools
- Adjust subagent tool scopes across profiles for explicit MCP access

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

Add structured logging for Ollama chat errors ...

Log model, message count, tools count, and raw error string whenever
self._client.chat() raises an exception. This makes it possible to
reconstruct the exact request payload that triggered a 500 from
Ollama Cloud — critical for diagnosing transient vs systemic failures.

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

Refactor profile tool config to explicit agent/subagent structure ...

Replaces the confusing mix of enabled_tools + mcp_servers + subagent_tools
with a single explicit structure:

    tools: {
      agent:   {native: [...], mcp: {server: [groups]}},
      subagent:{native: [...], mcp: {server: [groups]}}
    }

Why:
- Old fields mixed native and MCP names (mcp__server__tool) in one list,
  making it impossible to tell at a glance what a subagent actually gets.
- subagent_runner.py had 25 lines of runtime MCP filtering logic that
  was hard to follow and error-prone.

Changes:
- AgentProfile: add ToolConfig / ToolScopeConfig pydantic models,
  keep old fields (enabled_tools, mcp_servers, subagent_tools) for
  auto-migration via _migrate_tools validator.
- loader.py: read new "tools" key, auto-migrate legacy configs.
- agent.py: _tool_list now accepts ToolScopeConfig.
- subagent_runner.py: simplified — profile.get_subagent_tools() returns
  the exact scope, no runtime filtering needed.
- context_builder.py, list_tools.py, spawn_agent.py: updated to use
  profile.get_agent_tools() / get_subagent_tools().
- All 6 profile config.json files migrated to new schema.
- Secretary subagent now explicitly gets navi-web MCP tools for web search.

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

Fix planning: change plan-follow-up role from system to user ...

After injecting the plan as an assistant message into session.context,
the previous code appended a system message saying "Plan is ready.
Execute it now..."  Many instruct-tuned models treat their own
assistant message as a completed response, and a trailing system
instruction is easy to ignore.

Changing the follow-up to role="user" makes the model see:
  assistant: plan
  user: "Execute this plan..."
which obligates the model to produce a new assistant response —
the tool-calling execution phase.

The follow-up message is appended only to session.context (LLM
context) and never to session.messages, so it is invisible in the
chat UI.

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

Fix session file download URL — reverse legacy redirect ...

The webclient requests files at /api/sessions/{id}/files/{name},
but the actual endpoint lives at /sessions/{id}/files/{name}.
The old legacy redirect pointed the wrong way (/sessions → /api),
which always 404'd because /api/sessions/... was never registered.

- Replace legacy redirect with /api/sessions/... → /sessions/... (307)
- 307 preserves the request method and cookies during the redirect

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

Fix stop button responsiveness and shutdown CancelledError ...

Agent loop (_execute_tools_with_sink):
- Poll stop_event every 1s while draining the event sink via asyncio.wait_for
- When stopped, cancel the tool task, yield a synthetic ToolEvent failure,
  append a cancellation message to session, yield StreamStopped, and return
- Pass stop_event into _execute_tools_with_sink call site

Subagent runner:
- Check stop_event at the start of each tool in turn_tool_calls loop
- Returns early with ("", False) when stopped mid-batch

McpManager.disconnect_all():
- Disconnect clients sequentially instead of asyncio.gather
- Handle asyncio.CancelledError per-client to avoid shutdown traceback

AppContainer.shutdown():
- Catch BaseException instead of Exception for MCP and DB cleanup

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

Fix token counting: show only completion tokens, not cumulative prompt+completion ...

The token_count displayed next to assistant messages was summing
prompt_tokens + completion_tokens across ALL tool-calling iterations,
giving hundreds of thousands of tokens for multi-turn conversations.

Now:
- token_count (coins icon) = only completion tokens generated by the model
- context_tokens (ContextBar) = only prompt tokens (context size sent to LLM)

This gives users a realistic measure of how much the model actually generated.

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

Migrate MCP tool naming from mcp:server:tool to mcp__server__tool ...

The colon separator (mcp:server:tool) confuses many LLMs during
tool-calling because colons appear in schemas and URLs. Switch to
double-underscore separator (mcp__server__tool) for robust parsing.

Key changes:
- navi/mcp/tools.py: add build_mcp_name(), parse_mcp_name(), is_mcp_tool()
- navi/core/tool_executor.py: update _resolve_tool() with new helpers
  and legacy colon fallback for old sessions
- navi/core/tool_utils.py, subagent_runner.py: use build_mcp_name()
- navi/api/routes/{admin,agents}.py: prefix via build_mcp_name()
- navi/tools/{list_tools,reload_tools}.py: migrated
- All profile configs + system_prompt.txt: replace mcp: with mcp__
- manuals/{model_3d,lint_scad,render_3d,spawn_agent}.md: updated
- mcp_servers.d/gnexus-book.json: instructions updated
- docs/{api,profiles,tools,mechanics,visual.html}: updated
- tests: test_tool_executor.py and test_mcp.py aligned

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

SubAgentRunner: filter mcp_servers against subagent_tools whitelist ...

When a profile defines subagent_tools (strict whitelist for sub-agents),
MCP servers were still expanded unconditionally, granting sub-agents access
to MCP tools not listed in the whitelist.  Now:

- If subagent_tools contains mcp:xxx entries, only those specific MCP tools
  are passed to build_tool_list.
- If subagent_tools is non-empty but contains no mcp: entries, mcp_servers
  is set to None — sub-agents get no MCP tools at all.
- If subagent_tools is empty (fallback to enabled_tools), full mcp_servers
  is kept for backward compatibility.

400 passed, 1 skipped

FallbackOllamaBackend: do not blacklist single server, empty file fallback ...

- When only one Ollama server is configured, LLMConnectionError no longer
  adds it to the dead-server blacklist. This fixes the bug where a
  transient failure permanently blocked all requests until server restart.
- LLMModelNotFoundError on a single server is also not blacklisted.
- _discover_backends now falls back to settings.ollama_host when the
  ollama_backends_file is empty, missing, or returns no valid servers.
- Added unit tests covering single-server no-blacklist, multi-server
  blacklist, model-not-found no-blacklist, and empty-file fallback.

400 passed, 1 skipped

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

Fix UnboundLocalError: create mcp_manager before build_default_registries ...

The previous commit passed mcp_manager to build_default_registries but
left the instantiation after the call, causing UnboundLocalError at
runtime. Move McpManager() creation before the registry build and
remove the now-obsolete post-hoc _mcp_manager patching loop.

392 passed, 1 skipped

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

MCP: cache config in McpManager, add exponential backoff to McpClient reconnect ...

McpManager:
- Cache loaded configs in self._configs (loaded once at load_all)
- resolve_group() and get_instructions() read from cache instead of disk
- reload_all() busts the cache before re-reading
- Fallback to disk when cache is empty (tests / first call without load_all)

McpClient:
- Exponential backoff on reconnect: base 1s, max 30s, ±20% jitter
- Backoff resets on successful connect, doubles on failure
- _ensure_connected() blocks reconnect if within backoff window
- Prevents thundering herd against a flapping MCP server

392 passed, 1 skipped

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

DRY: unify tool execution in ToolExecutor._execute_one() ...

Three methods (_run_single_tool, _execute_tool_calls,
_execute_tool_calls_streaming) duplicated identical logic:
resolve → middleware → execute → image extraction → build message.

- Extract canonical _execute_one(tc, tool_map) -> (ToolEvent, Message, image_msg)
- All three public methods now delegate to _execute_one
- Public signatures unchanged — no test or caller changes needed

392 passed, 1 skipped

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

Eliminate cross-registry patching in registry.py via proper creation order ...

- Reorder build_default_registries so profiles and cp_registry are created
  BEFORE tools that need them
- All tools now receive full dependencies at construction time:
  ListToolsTool(profile_registry=profiles, mcp_manager=mcp_manager)
  SpawnAgentTool(backend_registry=backends, ...)
  ReloadToolsTool(cp_registry=cp_registry, mcp_manager=mcp_manager)
- Remove all post-creation patch lines (_profile_registry, _backend_registry, _cp_registry)
- Add mcp_manager parameter to build_default_registries
- Update create_container to pass mcp_manager

392 passed, 1 skipped

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>

Fix PgSessionStore import in container.py ...

`PgSessionStore` lives in `navi.core.pg_session_store`, not `navi.core.session`.

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>

Add legacy redirect for session files and fix STL viewer error handling ...

- Add /sessions/{id}/files/{filename} → /api/sessions/{id}/files/{filename}
  redirect in main.py for backward compatibility with old persisted URLs
- Fix STL viewer: wrap all renderer-dependent code in `if (renderer)`
  to prevent cascading errors when WebGL is unavailable
- Rebuild dist

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