refactor: migrate MCP config to directory-based mcp_servers.d ...

Replaces monolithic mcp_servers.json with per-server files in
mcp_servers.d/<name>.json. Filename stem becomes the server name.

- load_mcp_servers() reads directory globs, auto-migrates legacy file
- save_mcp_servers() writes per-server files, cleans up stale ones
- Update docstrings in manager.py and context_builder.py

Auto-migration: existing servers (gnexus-book, navi-3d, navi-web) plus
new ones (project_health, time_toolkit) now live in mcp_servers.d/.

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

Add session search across messages with backend + frontend ...

Backend:
- GET /sessions now accepts `search` query param
- _session_summary computes match_indices and match_preview from messages
- pg_session_store: messages ILIKE added to search_list and count_all
- In-memory store: search_list also filters by message content

Frontend:
- AppSidebar: search toggle icon + debounced input, Ctrl+K shortcut
- SessionItem: highlight matching text, show match_preview from search
- SessionList: pass searchQuery to SessionItem
- SessionsStore: searchQuery/searchActive state, setSearch/clearSearch
- API layer: getSessions accepts search param
- MessageList: scroll to target message + brightness flash animation
- ChatStore: loadSession accepts targetMessageIndex, scrollToMessageIndex ref
- CSS: msg-flash keyframe animation in app.scss
- Tests updated for new getSessions signature

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

Persist uploaded files in messages, live file tree updates, and UI polish ...

Backend:
- Add `files` field to `Message` model so uploaded file metadata survives page refresh
- Pass `files` through websocket handler → `agent.run_stream` / `agent.run`
- `list_tools`: make `profile_id` required; return error instead of all-tools fallback

Webclient:
- Call `fetchFiles()` after successful file upload for immediate Files tab update
- Live refresh file tree on filesystem (write/edit/append/mkdir/rm/cp/mv), terminal, and code_exec tool calls
- Add manual refresh button (desktop) and pull-to-refresh (mobile) to Files tab
- Fix live link updates: move regex creation inside per-message loop to avoid lastIndex state leak
- Restore full profile name text next to avatar in ChatHeader; hide avatar in header
- Fix mobile ArtifactsPanel: collapse tab text labels so close button fits with 3 tabs

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

Add profile_id support to list_tools ...

ListToolsTool now accepts an optional `profile_id` parameter. When
provided, it returns only the tools enabled for that specific profile
(enabled_tools + user tools + resolved MCP tools). This helps the agent
preview what a profile can do before switching.

- Updated ListToolsTool.execute() with profile-aware filtering
- Patched _profile_registry in build_default_registries
- Patched _mcp_manager in main.py startup loop

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

Fix gnexus-book MCP instructions and add old-format fallback in tool executor ...

- Updated mcp_servers.json gnexus-book instructions to use mcp:gnexus-book:
  prefix instead of the old mcp_gnexus-book_ format.
- Added fallback in tool_executor.py for old underscore format
  (mcp_server_tool → mcp:server:tool) so transitional models still work.
- Added unit test for the old-format fallback.

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

Generate session titles in the user's language ...

Adds "Respond in the same language as the user's messages" to the
session title generator system prompt so titles match the conversation
language instead of defaulting to English.

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

Fix agent.py _tool_list to use colon-delimited MCP names ...

The main registry and API routes were migrated, but Agent._tool_list
still built names with the old underscore format. This meant MCP tools
were silently dropped from the tool list passed to the LLM, causing
"tool not found" when the model correctly called mcp:server:tool names.

Also updates stale docstring in McpTools.

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>

Migrate web tools (web_search, web_view, http_request) to navi-web MCP server ...

New MCP server: mcp-servers/navi-web/
- app/search.py    — SearXNG primary, DDG fallback, Brave tertiary
- app/browse.py    — Playwright headless browser page extraction
- app/request.py   — httpx raw HTTP requests
- app/mcp_server.py — FastMCP entry point with stdio transport
- pyproject.toml   — deps: mcp, httpx, ddgs, playwright, pydantic

Changes:
- Added "navi-web" block to mcp_servers.json (stdio transport)
- Removed web_search, web_view, http_request from built-in registry
- Removed them from navi/tools/__init__.py
- Removed them from enabled_tools / subagent_tools in all profiles
- Added "navi-web": ["search", "browse", "request"] to mcp_servers
  in all profiles (developer, secretary, server_admin, tool_developer,
  modeler_3d, discuss)

Tests: 240 passed.

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

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>

Handle MCP tool aliases robustly

Clarify knowledge persistence prompts

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>

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>

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>

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>

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>

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>

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>

Add pagination, search, and sorting to admin sessions ...

Backend:
- Add count_all and search_list abstract methods to SessionStore
- Implement count_all and search_list in PgSessionStore (SQL with ILIKE)
- Implement count_all and search_list in InMemorySessionStore
- Update /admin/sessions to accept limit, offset, search, sort_by, sort_order
- Return {total, limit, offset, items} from /admin/sessions

Frontend:
- Add search input for sessions in admin panel
- Add clickable sortable column headers with asc/desc toggle
- Add pagination controls (prev/next, page size selector, item count)
- Debounce search input (300ms)

Tests:
- Add integration tests for pagination, offset, search, and sorting
- All 217 tests pass

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

Propagate user profile to LLM context via current_user_info ContextVar ...

- Extend User model: username, first_name, last_name, phone, birth_date,
  country, city, locale (all from gnexus-auth profile)
- navi_users DDL: add new profile columns
- auth/deps + auth/callback: populate new fields on upsert
- /auth/me: return all profile fields
- Add current_user_info ContextVar for full user profile propagation
- websocket + messages: set current_user_info before agent.run()
- run_ephemeral: inherit and restore current_user_info
- ContextBuilder: _user_context_msg() injects [User context] with name,
  email, location, locale, role into LLM system messages
- _security_policy_msg: reads user_id/role from ContextVar directly

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

Add multi-user sandbox: filesystem, terminal, code_exec, security policy ...

- filesystem, share_file: sandbox non-admin users to user_data/<user_id>/
- terminal: working_dir sandbox + allowlist + dangerous pattern block for users
- code_exec: sandbox CWD and temp files to user_data/<user_id>/ for users
- context_builder: inject dynamic security policy into LLM context (user/admin)
- config: terminal_user_allowed_commands setting
- agent: wire user_id/user_role through ContextBuilder.build()
- base: add current_user_role ContextVar; run_ephemeral inherits role

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

Add per-user filesystem sandbox via current_user_id ContextVar ...

- tools/base.py: add current_user_id ContextVar (set by Agent before
  every tool call, cleared after)
- core/agent.py: set current_user_id in run_stream from session.user_id
  and in run_ephemeral from parent_session.user_id; restore in finally
- tools/filesystem.py: _check_path resolves all paths inside
  user_data/<user_id>/ when current_user_id is present; legacy mode
  (no user_id) falls back to FS_ALLOWED_PATHS
- tools/share_file.py: validate source path is inside user sandbox

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

Fix NameError in run_ephemeral: session was undefined ...

run_ephemeral doesn't have a session variable. Pass user_id from the
parent session (looked up via parent_session_id) instead of referencing
non-existent session variable.

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

Fix legacy session visibility and add WebSocket auth debug logging ...

- pg_session_store: remove OR user_id IS NULL from list_all/list_page
  so legacy sessions are no longer visible to all users
- auth/deps.py: add debug logging at every step of _resolve_user
- websocket.py: add debug logging at every stage of websocket_session

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

Multi-user auth via gnexus-auth OAuth + hybrid role/permission model ...

- Integrate gnexus-auth-client-py (GAuthClient) for OAuth flow, token refresh,
  and webhook parsing
- Add navi/auth/ package: User model, Fernet encryptor, client singleton,
  deps (get_current_user, require_admin, require_permission)
- New tables: navi_users, user_auth_sessions (auto-created on startup)
- Session/memory isolation by user_id with legacy NULL support
- Cookie-based auth proxy: /auth/login, /callback, /logout, /me
- Webhook receiver /webhooks/gnexus-auth handling user events, global logout,
  session revocation, role/permission changes
- Admin endpoints (/admin/*) gated by role + permissions
- Webclient auth store with isAdmin/hasPermission guards
- Admin-only profile filtering in /agents/profiles
- 200/200 tests passing

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

Paginate session list loading

Refine 3D modeler workflow

Simplify 3D SCAD subagent prompt