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>

Mark architecture weak spot #10 (MCP caching/backoff) as resolved ...

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>

Mark architecture weak spot #7 (DRY tool_executor) as resolved ...

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>

Mark architecture weak spot #6 (cross-registry patching) as resolved ...

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>

Mark architecture weak spot #5 (duplicate PostgreSQL pools) as resolved ...

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>

Mark architecture weak spot #4 (mutable settings) as resolved ...

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>

Mark architecture weak spots #2 and #3 as resolved ...

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>

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>

Fix SyntaxError: Illegal return statement in STL viewer ...

The previous fix replaced `throw err` with `return` inside a module,
but top-level `return` is a SyntaxError in ES modules.
Reverted to `throw err` — the error message is already shown on screen,
so the user still gets a graceful fallback even though the error appears
in the console.

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 5-7: Extract async generators from run_stream, unify run() as wrapper ...

- _compression_events_preturn / _compression_events_midturn
- _consume_stream (uses StreamState)
- _execute_tools_with_sink
- run() is now a thin wrapper around run_stream() collecting StreamEnd
- Remove dead imports (json, LLMChunk)
- Mark god-object decomposition complete in architecture_weak_spots.md

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>

Step 2: Extract AgentTurnContext dataclass from run_stream() ...

Move 10 turn-level local variables from run_stream() into AgentTurnContext:
- turn_start, tool_call_count, turn_tokens, subagent_tokens
- stall_no_todo, stall_repeat_tools, prev_tool_sigs
- known_failed, replan_msg, injected_fact_ids

This makes run_stream() readable and prepares the ground for
AntiStallMonitor (Step 3) which will consume this context.

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>

Add comprehensive mechanics catalog (docs/mechanics.md) ...

Master catalog of all mechanisms in the Navi project:
- 80+ mechanics catalogued across all subsystems
- Each with description, config flags, source files, documentation status
- 50 undocumented mechanics explicitly listed
- Cross-reference index for feature planning
- Updated docs/index.md to link the catalog

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

Fix scratchpad get_section user_id and filesystem diff newline bugs ...

- get_section: use _uid() instead of None so multi-user lookups match
  the user_id-scoped writes done by the scratchpad tool execute()
- filesystem _diff: remove erroneous [l + \"\\n\"...] wrappers around
  splitlines() output; difflib.unified_diff already handles line lists

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

Add inherit_system_prompt and is_subagent_only mechanisms ...

- inherit_system_prompt: subagent parameter to prepend parent's system
  prompt as a base layer before subagent specialisation
- is_subagent_only: profile flag blocking switch_profile, allowing
  spawn_agent only; shown with [subagent only] tag in list_profiles
- Document both in docs/profiles.md and docs/tools.md

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>