tools: split filesystem into read, write and file_ai ...

- filesystem_read: read, list, find, find_up, grep, info, exists, diff
- filesystem_write: write, append, edit, edit_lines, insert, mkdir, move, copy, delete
- file_ai: ask (was query), edit (was smart_edit)
- paged numbered reads (500 lines / 50 KB), raw copy mode, binary refusal
- nearest-match and numbered-copy hints on failed edits, context after edit
- guards: empty overwrite, non-empty delete, move/copy overwrite
- cross-tool redirects instead of silent wrong-action errors
- legacy 'filesystem' stays for archived sessions (compression, renderers, webclient)
- profiles, prompts, docs and manuals updated; TUI and webclient render the new tools

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raw excerpt that a newer curated fact overrides is labelled outdated rather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.

port: 8000/8001 -> 8099/8098 everywhere ...

navi runs on shared servers where 8000/8001 are usually taken. New
defaults: API 8099, navi_ui MCP 8098. Touched: config defaults
(navi_port, navi_ui_mcp_port, public_url, gnauth_redirect_uri),
navi-server launcher docs, env.template/.env.example, install.sh
health-check fallback, terminal client base_url, webclient dev configs
(useWebSocket, contentLinks, vite proxy), android url hint, docs.
Also made the navi_ui FastMCP constructor port settings-driven instead
of a hardcoded 8001 (it was overridden at start anyway).

docs: sync with the plan rework and compression pipeline ...

- planning: plan tool flow (agent-invoked, no pre-turn gate), confirmation
  by COMPLEXITY, think=False + 20k-char Phase 1 window, retired flags
  removed from profiles/api docs
- compression: all four triggers through compress_and_save_session,
  real-baseline gates, head+tail summary input, _plan_compression shared
  decision, actual config defaults (0.90 threshold, 6000 summary tokens,
  32k input cap)

docs: document bounded autonomy + navi-code TUI features ...

- profiles.md: new "Bounded autonomy" section (scope_boundary_enabled,
  observe_skips_plan_enabled) + memory-facts scope filter; navi_code section
  and config.json example updated
- mechanics.md: Agent Loop / Planning Pipeline / Context Builder rows for
  scope boundary, observe short-circuit, MODE classification, scope filter
- navi_code.md: bounded autonomy note in profile section
- navi_code_cli.md: --raw and -h/--help params, multiline input, planning
  and spawn_agent cards, nested subagent styling, planning_status/plan_ready/
  turn_thinking rendering, tui/renderers/ in dev section

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

docs: update docs for tools.agent/tools.subagent and Navi Code TUI ...

- profiles.md: document tools.agent/tools.subagent structure, deprecate enabled_tools
- tools.md: move web tools to MCP section, fix mcp__navi-web__* names, add create_mcp_server/test_mcp_tool/mcp_status/recall tools
- api.md: update /agents/profiles and /admin/profiles/{id} response schemas, fix MCP examples
- navi_code.md: correct navi_code tool list (MCP disabled)
- navi_code_cli.md: add /thinking, /compact, correct TUI layout
- index.md: add navi_code, terminal client, pydantic-settings
- testing.md: refresh test directory layout, replace stale coverage roadmap
- agent.md: mention tools.agent/tools.subagent in loop

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

Update Navi Code profile: config, prompts, docs, and env example ...

- Sync navi_code profile tools with current codebase (memory, schedule_recall, manage_recall, switch_profile, list_profiles)

- Remove image_view and MCP tools from navi_code; keep local terminal focus

- Update system prompt and persona for terminal-first coding assistant

- Update docs/navi_code.md, docs/profiles.md, docs/config.md for new tool set

- Refresh .env.navi_code.example with current config variables

- Remove stale CLI prototype directories (cli/, navi_code_cli/)

Docs: actualize navi_code tool lists and key_tools ...

- docs/navi_code.md and docs/profiles.md now correctly list native tools,
  MCP navi-web tools, and excluded tools.
- image_view is documented as enabled for the agent (loads and describes
  images for the model, not shown to the user).
- web_search/http_request are documented as MCP navi-web tools, not native
  disabled tools.
- navi/profiles/navi_code/config.json: updated full_description.key_tools to
  match actual resolved tool names.

Tests: 459 passed, 1 skipped.

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

Navi Code: Phase 2 — CLI terminal client, tests, docs ...

- Add clients/terminal package: config, state, REST API wrappers, WebSocket
  client, renderer, and click-based interactive CLI.
- Wire navi-code console script via pyproject.toml.
- Add unit and WebSocket integration tests for the terminal client.
- Update docs/profiles.md, docs/config.md, README.md with navi_code profile
  and default-profile instructions.
- Add docs/navi_code.md setup guide and docs/navi_code_cli.md usage reference.
- Fix lint in new test files and test_auth_disabled.py.

Tested: 459 passed, 1 skipped (excluded unrelated websocket test).

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