memory: one search across facts, raw history and sketches ...

Compression removes messages from the model's window, not from the
conversation: every compression path now writes the turns it demotes into
`memory_chunks` — verbatim, append-only, with the turn range, timestamps and
breadcrumb keys (the summarizer's `KEYS:` line plus a deterministic extractor,
which also covers the hard-truncate fallback that never sees a summarizer).

`memory_search` is the single read path over the three stores: curated facts
first, then raw excerpts by relevance, then the current session's sketches.
Every hit carries provenance (source, session, turn range, timestamp), and a
raw excerpt that a newer curated fact overrides is labelled outdated rather
than hidden — "we changed our mind, the old value was X" is often the
question. The agent also gets up to two relevant excerpts injected per turn
once the context holds a summary, deduped across turns.

Fixes found by running the pilot against a real database:
- `search_facts` returns ISO-string timestamps while chunks return datetimes;
  the freshness comparison raised TypeError and took the whole search down.
- an existing `memory_chunks` table created without pgvector never gained the
  `embedding` column (CREATE TABLE IF NOT EXISTS does not alter), and the
  INSERT failed on it; the DDL now adds the column, and a database without
  pgvector writes text-only rows found through FTS.

cleanup: remove deprecated tools and orphaned memory tools ...

Removed (no profile used them, no cross-dependencies):
- write_tool.py, delete_tool.py, test_tool.py
- memory_save.py, memory_search.py, memory_forget.py

Updated:
- navi/core/registry.py — removed imports and registrations
- navi/tools/__init__.py — removed imports
- docs/tools.md — removed references, updated self-extension section to MCP
- navi/tools/tool_manual.py — updated example to create_mcp_server

Profile fixes:
- developer: +tool_manual, +ssh_exec
- discuss: +list_profiles
- tool_developer: +mcp_servers navi-web

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 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>

Restructure persona: concrete information gathering protocol ...

- Replace abstract CONTEXT FIRST principle with explicit numbered protocol
  (check summary → memory_search → NAVI.md → ask user)
- Move protocol to top of persona (after identity) so it has maximum weight
- NAVI.md section: remove READ instructions (now in protocol), keep only WRITE
- LONG-TERM MEMORY: remove "search proactively" line (now in protocol),
  keep only save/forget instructions
- memory_search description: remove misleading "call at start of each session"
  (summary is already auto-injected); clarify when to actually call it

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

Add long-term user memory system ...

Architecture:
- navi/memory/store.py: MemoryStore backed by SQLite (memory_facts,
  memory_summary, session_memory_state tables in navi.db)
- navi/memory/extractor.py: LLM-based fact extraction from sessions +
  summary regeneration (triggered after session goes idle >30 min)
- Fact upsert uses UNIQUE(category, key) — same key always overwrites,
  no duplicates or stale contradictions
- Keyword search across category + key + value (LIKE-based, no extra deps)

Context injection:
- Memory summary injected as an ephemeral system message on every LLM call
  via Agent._with_memory() — never persisted to session.context

Tools (all profiles):
- memory_search(query): keyword search against fact DB; persona instructs
  model to call it at session start and before personal-context questions
- memory_forget(key, category?): delete a specific fact on user request

Extraction trigger:
- On new session creation, fire-and-forget background task checks all
  sessions idle >30 min with unprocessed messages → runs extraction

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