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>

Increase max_iterations across all profiles ...

- developer: 45 → 100
- discuss: 12 → 30
- modeler_3d: 50 → 70
- secretary: 35 → 70
- server_admin: 40 → 100
- tool_developer: 35 → 100

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

Add absolute rule: gnexus-book must be edited only through MCP tools ...

- persona.txt: add EXTERNAL KNOWLEDGE BASES block with absolute prohibition
  on filesystem/terminal/code_exec for gnexus-book; only MCP tools allowed
- mcp_servers.json: add ABSOLUTE RULE section to gnexus-book instructions
  with explicit tool mapping and NEVER clause for direct file access

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>

Wire MCP manager into sub-agent (spawn_agent) so MCP tools are available to sub-agents ...

- SpawnAgentTool: add mcp_manager parameter and pass it to Agent
- main.py: patch _mcp_manager into spawn_agent after MCP connect

Fixes: tool 'mcp_gnexus-book_*' not found in sub-agent sessions.

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

Handle MCP tool aliases robustly

Clarify knowledge persistence prompts

Fix JSON syntax in mcp_servers.json ...

Escape literal newlines inside the instructions string.

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

Integrate proactive knowledge capture into planning and persona ...

- Phase 1 planning: add KNOWLEDGE CAPTURE section to prompt
- Phase 3 planning: add knowledge persistence rule with target selection
- Persona: add "search before save" deduplication instruction
- MCP gnexus-book: add persistence guidance for discovered facts

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

Rebuild dist after resolving merge conflicts ...

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

ready dist

Rename login button text from gnexus-auth to GNEXUS. ...

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

Fix Phosphor icon class on GnButton/GnIconButton usages. ...

gnexus-ui-kit's iconNode() does not prepend the base `ph` class
when the icon string starts with `ph-`; it only keeps the string
as-is. All icon props must include the base class explicitly:
`icon="ph ph-sidebar"` instead of `icon="ph-sidebar"`.

Updated 15 icon bindings across 9 components.

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

Wire gnexus-ui-kit v0.2.0 Vue 3 adapter and migrate Wave 1 components. ...

- Update vendor/gnexus-ui-kit to v0.2.0 (Vue components + composables)
- Add Vite aliases for gnexus-ui-kit/vue and gnexus-ui-kit/css
- Install GnexusUiVue plugin in main.js + GnToastProvider in App.vue
- Migrate ProfileBadge → GnBadge
- Migrate ErrorMessage → GnAlert
- Migrate ConfirmDialog → GnConfirmDialog
- Migrate raw <button> elements → GnButton / GnIconButton in:
  WelcomeScreen, LoginScreen, ChatArea, ChatHeader, AppSidebar,
  ArtifactsPanel, UserMessage, AssistantMessage, SelectionToolbar

Build and tests pass (51/51).

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

Auto-inject relevant memory facts into LLM context on every user turn. ...

Semantic search against the vector memory store runs in parallel with
context provider collection. Number of injected facts scales with
message length (1–3) to reduce noise on short queries. Guardrails:
min length gate, per-turn deduplication, and structured logging at
info level for observability.

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>

Remove dead LLMBackend.stream() method ...

The method was defined on all backends (Ollama, FallbackOllama, OpenAI)
and in the base LLMBackend interface, but was never called by agent.py
or messages.py. stream_complete() covers all streaming use cases.

- navi/llm/base.py: remove abstract stream() method
- navi/llm/ollama.py: remove OllamaBackend.stream()
- navi/llm/fallback.py: remove FallbackOllamaBackend.stream()
- navi/llm/openai_backend.py: remove OpenAIBackend.stream()
- docs/tech_debt_review: mark item 54 as fixed

236 tests passing.

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

Fix ollama_backends / FallbackOllamaBackend issues ...

- registry.py: always use FallbackOllamaBackend (unified backend).
  Enables model priority lists in all deployments, not just multi-server.
- agent.py: add missing think=profile.think_enabled to run() (REST endpoint).
- compressor.py: fix model param type (str → list[str] | str | None).
- fallback.py: harden load_servers_from_file against missing/bad JSON files
  and entries without host. Add clear_blacklists() for manual reset.
- admin.py: add POST /admin/ollama/clear-blacklists endpoint.
- tech_debt_review: document dead stream() methods.
- tests: add tests for single-server fallback, bad file handling,
  missing host skipping, and blacklist clearing.

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

Add deterministic line-based file editing (edit_lines), rating UI fix, and session refresh ...

- filesystem.py: add edit_lines action (deterministic line ops via operations array)
           + numbered param for read (1-based line numbers in output)
           + clarify four editing modes in tool description
- chat.js: fix rating IDs for streaming messages (assign h_ ID on stream_end)
- SessionList.vue: mobile pull-to-refresh with PTR_THRESHOLD=80
- AppSidebar.vue: desktop refresh button next to Conversations header
- planning.py: knowledge source assessment in Phase 1
- debug panel: MCP servers tab + resolved tools per profile
- NAVI.md: reposition as neutral quick-reference

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>

Fix MCP tool lookup in websocket handler and tests ...

- websocket.py: pass mcp_manager to Agent(), with graceful fallback
  if MCP connection fails
- conftest.py: mock get_mcp_manager() in tests to prevent SSE
  connection attempts against real servers

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

Refactor MCP integration: server groups in profiles ...

- mcp_servers.json: add 'groups' (read/write/admin) for gnexus-book
- AgentProfile: new 'mcp_servers' field (server_name -> group list)
- Profile loader: parse and persist 'mcp_servers' in config.json
- Agent._tool_list(): expands mcp_servers into concrete tool names
  via McpManager.resolve_group(), wildcard '*' supported
- /agents/profiles API: includes 'mcp_servers' in response
- Profiles no longer list individual mcp_ tools in 'enabled_tools'
- discuss: gnexus-book read group
- server_admin: gnexus-book read+write+admin groups

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

Connect gnexus-book MCP server and enable in profiles ...

- mcp_servers.json: SSE transport to 192.168.1.170:8001
- server_admin profile: all 16 gnexus-book tools
- discuss profile: read-only gnexus-book tools (docs + inventory)

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>

Rebuild webclient and fix showWelcome condition ...

- Rebuild dist/ after removing erroneous vue-router
- Fix App.vue showWelcome to use chatStore.loading (prevents flicker
  to WelcomeScreen during session load)

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

Remove erroneous vue-router from webclient ...

vue-router was accidentally left over from an earlier attempt to embed
admin features in the main client. It broke hash-based session routing
and rendered app-main empty. Revert to direct component rendering in
App.vue with native hashchange handling.

- Remove vue-router dependency and src/router/index.js
- Revert main.js to createApp without router
- App.vue: render WelcomeScreen/ChatArea directly, restore hashchange handler
- chat.js: revert hash format to raw session id
- api/index.js: keep 401 → authStore.user = null (login overlay fix)

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

Fix blank session rendering and 401 auth handling ...

- Install missing vue-router dependency (was imported but not in node_modules,
  causing app init failure and empty app-main)
- Add :sessionId? route param and HomeView watcher for hash-based session routing
- Update hash format to '#/' for Vue Router compatibility
- Add 401 handling in api/index.js to invalidate auth and show login overlay
- Add error handling in loadSession and WelcomeScreen start to prevent stuck UI

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

Replace profile edit drawer with centered modal ...

The drawer was awkward on wide screens. Modal is centered, capped at
900px, with proper header/body/footer layout and scrollable content.
Model & Generation fields now render in a responsive row of 5 columns.

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

Add profile editing to admin panel ...

Backend:
- navi/profiles/loader.py: add save_profile_to_dir() to write config.json
  and system_prompt.txt back to disk
- navi/core/registry.py: add ProfileRegistry.update() for in-memory updates
- navi/api/routes/admin.py: new endpoints GET /admin/profiles/{id} and
  PUT /admin/profiles/{id} for reading and saving full profile config

Admin panel:
- Profiles table: add Edit button per row
- Drawer form with sections: Basic, Model & Generation, Thinking,
  Planning, Sub-agent, Tools, System Prompt
- All fields editable inline (text inputs, checkboxes, textareas for lists)
- Save via PUT request, updates both disk and in-memory registry without
  server restart

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