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>

Migrate MCP tool naming from mcp:server:tool to mcp__server__tool ...

The colon separator (mcp:server:tool) confuses many LLMs during
tool-calling because colons appear in schemas and URLs. Switch to
double-underscore separator (mcp__server__tool) for robust parsing.

Key changes:
- navi/mcp/tools.py: add build_mcp_name(), parse_mcp_name(), is_mcp_tool()
- navi/core/tool_executor.py: update _resolve_tool() with new helpers
  and legacy colon fallback for old sessions
- navi/core/tool_utils.py, subagent_runner.py: use build_mcp_name()
- navi/api/routes/{admin,agents}.py: prefix via build_mcp_name()
- navi/tools/{list_tools,reload_tools}.py: migrated
- All profile configs + system_prompt.txt: replace mcp: with mcp__
- manuals/{model_3d,lint_scad,render_3d,spawn_agent}.md: updated
- mcp_servers.d/gnexus-book.json: instructions updated
- docs/{api,profiles,tools,mechanics,visual.html}: updated
- tests: test_tool_executor.py and test_mcp.py aligned

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

docs/profiles: document subagent_tools MCP filtering behavior ...

Clarify that subagent_tools acts as a whitelist for MCP tools:
- Only mcp: entries explicitly listed in subagent_tools are exposed to sub-agents.
- If subagent_tools is non-empty and contains no mcp: entries, the sub-agent
  receives no MCP tools at all.

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>

Rename MCP tools to mcp:server:tool format and restore human-readable names ...

- Core naming: mcp_server_tool → mcp:server:tool (colon-delimited)
- navi-web tools: search/view/request → web_search/web_view/http_request
- navi-3d tools: compile_scad/render_stl/lint_scad (unchanged names)
- Updated all profile configs, system prompts, docs, manuals, tests
- Added new lint_scad.md manual
- Fixed modeler_3d prompt stale references (scad_lint, model_3d, render_3d)
- All 240 tests pass

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

Clean up remaining web_search / web_view / http_request references ...

- Deleted stale source files: navi/tools/web_search.py, web_view.py,
  http_request.py (no longer imported or registered).
- Updated system_prompt.txt in all profiles (secretary, server_admin,
  discuss, modeler_3d subagent) to reference mcp_navi-web_* tool names.
- Updated key_tools in developer, secretary, server_admin config.json.
- Updated docs (tools.md, profiles.md, api.md) to reflect MCP migration.

Tests: 240 passed.

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

Audit and fix docs/ for accuracy against current codebase ...

Package A (API + WebSocket + Sessions):
- api.md: add missing endpoints (health/embed, auth/status, agents/prompts,
  agents/mcp_servers, sessions/content, 7 admin endpoints). Fix response
  schemas, auth requirements, query params. Update path formats.
- websocket.md: fix planning_status.phase type (int 1|2|3), add metadata
  to tool_call, message_index to stream_end, context_tokens/max_context_tokens
  to context_compressed.
- sessions.md: fix context_compression_threshold default (0.80→0.70),
  add list_page method, add metadata to Message flags.

Package B (Config + Profiles + Tools + Agent + Memory):
- config.md: remove stale ANTHROPIC_API_KEY description, add 12 missing
  env vars (embedding, web search, terminal_user_allowed_commands,
  context_providers_dir, gnauth fields, output_reserve_tokens).
  Fix OPENAI_BASE_URL type.
- profiles.md: fix max_iterations default (20→10), add top_k/top_p/num_thread,
  is_admin_only, context_providers, mcp_servers, subagent_think_enabled.
  Clarify subagent_tools fallback and step_validation_enabled.
- tools.md: replace 3 separate memory tools with unified `memory`, add
  `mcp_status`.
- agent.md: fix run_ephemeral return type (str→tuple), clarify DB reads.
- memory.md: fix search_facts/get_all_facts param order, fix MemoryStore
  init description.

236 tests passing.

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

Allow subagents to use selected profiles

Add 3D modeling profile with model_3d and render_3d tools ...

New profile:
- modeler_3d: 3D model design for 3D printing (OpenSCAD → STL)

New tools:
- model_3d: compile .scad → binary STL via OpenSCAD CLI
- render_3d: render PNG previews from STL (up to 3 views, 400×300)

Both tools return openscad_not_found error if OpenSCAD is not installed.

Docs:
- README.md: add modeler_3d to profile table
- docs/profiles.md: add modeler_3d to active profiles
- docs/tools.md: add model_3d and render_3d to builtin tools
- manuals/model_3d.md, manuals/render_3d.md: full usage manuals
- modeler_3d system_prompt.txt: OpenSCAD-first workflow with dedicated tools

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

Docs audit: fix outdated references (PostgreSQL, Vue client, profiles, tools) ...

- architecture.md: SQLite → PostgreSQL + pgvector
- README.md: vanilla JS → Vue 3 + Pinia, remove smart_home, update temps
- profiles.md: remove smart_home, add discuss, update temperatures
- tools.md: add missing built-in tools, update user tools list
- sessions.md: fix outdated references
- NAVI.md: sync with current stack
- persona.txt: update self-extension and content_publish guidance
- content_publish.md manual: reflect session_dir-based no-copy design
- content_store.py & content_publish.py: inline with docs

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

Add structured planning review and adaptive depth

Add per-phase planning flags and planning_mandatory ...

- planning_mandatory: disables DIRECT shortcut, forces all phases to run
- planning_phase1_enabled / phase2_enabled / phase3_enabled: per-phase toggles
- planning_phase2_enabled replaces planning_reflect_enabled (migrated in loader with backward compat)
- Migrate all profile configs; rewrite docs/profiles.md as full config reference

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

WelcomeScreen polish, root-path fix, docs update ...

- Move mobile sidebar button to top-left corner (no header bar backdrop)
- Show WelcomeScreen on / with no hash instead of auto-loading first session
- Docs: document Ollama multi-server fallback, model priority lists, OLLAMA_BACKENDS_FILE

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

Make server I/O non-blocking; update docs ...

- Wrap all heavy filesystem ops in asyncio.to_thread: filesystem tool
  (read/write/append/list/find/info/move/delete/query/smart_edit),
  image_view (read_bytes), share_file (shutil.copy2), write_tool
  (write_text, _register_user_tool), session_files (shutil.rmtree,
  iterdir), sessions upload endpoint (sync open/write → to_thread)
- Make delete_session_dir async; update its caller in sessions.py
- docs/config.md: fix wrong defaults (threshold 0.70, keep_recent 8),
  remove phantom SESSION_FILES_TTL_HOURS, add LLM timeouts, DATABASE_URL,
  PUBLIC_URL, Gmail, CONTEXT_SUMMARY_MAX_TOKENS sections
- docs/profiles.md: add missing tool_developer profile to table
- android-client: add WebView remote debugging; remove unused toolbar menu
- Remove stale helper scripts and test files

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

Use gemma4 cloud model by default

Add NAVI.md navigation hub and update core docs ...

NAVI.md: lightweight project entry point for Navi — server command,
key paths, doc map with query instructions, tool manual index.
All profiles read this; detailed content stays in docs/.

docs/agent.md: rewrite to cover 3-phase planning, all 10 thinking
mechanics flags, adaptive replan, anti-stall, goal anchoring.

docs/profiles.md: update AgentProfile fields (all flags), correct
profile list (secretary/server_admin/developer), JSON config format,
auto-discovery instead of manual registration.

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

Add backend documentation ...

10 markdown files covering all backend subsystems: architecture,
agent loop, tool system, sessions, WebSocket protocol, profiles,
memory, config, and API reference. Structured for AI readability
with a single entry point (docs/index.md) and cross-references.

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