Fix MCP tool registration at startup ...

Root cause: _on_mcp_server_connected was defined and registered AFTER
mcp_manager.load_all(), so startup connections never registered their
tools into the ToolRegistry.

Fix: explicitly iterate connected clients after build_default_registries()
creates tool_registry, and register their MCP tools before starting the
health-check loop. The callback stays for future reconnects.

Also adds diagnostic warning in build_tool_list when tools are missing.

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

Fix MCP tool availability after health-check disconnect/reconnect ...

- connect() now calls _cleanup() first to avoid stale transport leaks.
- mark_disconnected() clears _session so _ensure_connected() knows
  the client truly needs a fresh session.
- register_mcp_tools() is no longer a no-op; it re-registers all
  connected MCP tools so reload_tools correctly restores them.

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

Add MCP health check loop, auto-reconnect, and system toast notifications ...

Backend:
- McpManager: keep all configured servers in the pool even if connect()
  fails at startup; health-check loop (30s) tries to reconnect dead servers
  and verifies live ones with list_tools()
- McpManager: set_on_server_connected callback re-registers tools when a
  dead server comes back online
- McpClient: add mark_disconnected() for silent drop detection
- McpStatusTool: skip list_tools() for disconnected servers
- Orchestrator: broadcast mcp_status_update to all WebSocket sessions
- New event type McpStatusUpdate with server_name, status, tool_count

Webclient:
- useWebSocket: handle mcp_status_update → toast.success/toast.error

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

Fix MCP transport teardown race with anyio task groups

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>

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>

fix: wire test_mcp_tool into MCP manager startup injection ...

The startup loop in main.py assigns _mcp_manager only to tools that
have the attribute, but test_mcp_tool never declared it and mcp_status
used _manager instead of _mcp_manager — so both received None forever.

Changes:
- test_mcp_tool: add __init__(mcp_manager) with _mcp_manager, fallback
  to module-level import if startup wiring skipped
- mcp_status: rename _manager → _mcp_manager, same fallback
- registry.py: register create_mcp_server and test_mcp_tool builtins
- main.py: include test_mcp_tool in startup wiring loop
- client.py: add 5s timeout to disconnect cleanup

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>

Add auto-reconnect to MCP client on call_tool/list_tools ...

- McpClient._ensure_connected() reconnects if session is dead
- list_tools() and call_tool() try reconnect + one retry on failure
- Fixes crash when MCP server restarts between calls

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

Fix graceful MCP disconnect during server shutdown ...

- McpClient.disconnect(): catch CancelledError / RuntimeError from
  anyio SSE transport teardown
- McpManager.disconnect_all(): shield gather from CancelledError
- main.py _on_shutdown(): catch CancelledError and RuntimeError
  explicitly (BaseException, not Exception)

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

Inject MCP server instructions into system prompt ...

- McpClient: collect instructions from MCP initialize handshake
- McpServerConfig: add 'instructions' field for Navi-side overlay
- McpManager.get_instructions(): merge server + config instructions
- ContextBuilder: new _mcp_context_msg() injects MCP server
  descriptions into every LLM context as a system message
- Agent passes mcp_manager to ContextBuilder
- mcp_servers.json: add overlay instructions for gnexus-book

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>