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 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>

Wire pgvector semantic search into memory system ...

- Add vector(768) column + HNSW index to memory_facts

- Add LLMBackend.embed() with Ollama + fallback implementation

- MemoryStore: cosine-distance search with ILIKE fallback

- New memory tool params: source, confidence, expires_days, source_context

- Update extractor, sqlite_store, deps wiring

- Add pgvector to requirements

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

Consolidate memory_search/save/forget into single memory tool ...

Three separate tools → one tool with action enum (save/search/forget/list).
Reduces tool-slot pressure; same functionality, same MemoryStore backend.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>