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 self-recall (scheduled callback) system ...

Core features:
- schedule_recall tool: once/recurring/immediate callbacks
- manage_recall tool: cancel/skip/list scheduled recalls
- Natural-language time parser (ISO, relative, "tomorrow at 09:00")
- PostgreSQL-backed RecallScheduler with lazy pool init
- Background recall_scheduler_loop with asyncio.Semaphore(3)
- _busy_sessions guard prevents user messages during headless runs
- Agent.run() preserves thinking field for session history visibility
- API endpoints: GET/DELETE/POST for session recall, admin list
- Frontend: recall badge, filter, cancel/skip in sidebar and chat header
- Tests: parser, scheduler CRUD, tools, API, scheduler loop (53 tests)
- Manuals: schedule_recall.md and manage_recall.md

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

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1

chore: remove test MCP servers from repo ...

project_health and time_toolkit were created for development testing
and should not be part of the committed codebase.

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

merge

feat: MCP server template, manual, and example servers ...

Add canonical scaffolding for MCP server development:

- manuals/write_mcp_server.md: full guide covering structure, validation,
  smoke-testing, registration, and troubleshooting
- mcp-servers/_template/: annotated starter with annotated mcp_server.py
  and pyproject.toml for FastMCP + pydantic
- mcp-servers/project_health/: example server with 3 tools
  (get_project_summary, find_duplicate_files, get_project_dependencies)
- mcp-servers/time_toolkit/: example server with 4 tools
  (get_current_time, convert_timezone, add_time, format_datetime)

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

fix: wire test_mcp_tool into MCP manager startup injection ...

The startup loop in main.py assigns _mcp_manager only to tools that
have the attribute, but test_mcp_tool never declared it and mcp_status
used _manager instead of _mcp_manager — so both received None forever.

Changes:
- test_mcp_tool: add __init__(mcp_manager) with _mcp_manager, fallback
  to module-level import if startup wiring skipped
- mcp_status: rename _manager → _mcp_manager, same fallback
- registry.py: register create_mcp_server and test_mcp_tool builtins
- main.py: include test_mcp_tool in startup wiring loop
- client.py: add 5s timeout to disconnect cleanup

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

fix: filesystem empty path validation and terminal timeout defaults ...

filesystem:
- Reject empty string paths in _check_path to prevent writing to cwd
- Clear error message when 'write' action uses 'destination' instead of 'path'

terminal:
- Reduce default timeout from 300s to 20s
- Clamp user-provided timeout between 1 and 300s
- Update parameter description to mention max and common use-cases

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

feat: add create_mcp_server and test_mcp_tool builtins ...

create_mcp_server:
- Scaffolds mcp-servers/<name>/ directory with venv, pyproject.toml,
  app/__init__.py, and annotated mcp_server.py template
- Runs pip install -e . in isolated thread to avoid event-loop issues
- Validates template with python -m py_compile

test_mcp_tool:
- Execute a single MCP tool call for isolated testing
- Detailed diagnostics: not connected, empty response, timeout, crash
- Fallback to module-level _mcp_manager if startup wiring skipped

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

refactor: rewrite tool_developer profile for MCP server development ...

Complete migration from old-style user tools (tools/*.py) to MCP servers.

Profile changes:
- Replace write_tool, delete_tool, test_tool with create_mcp_server,
  test_mcp_tool, mcp_status, reload_tools
- Update system_prompt.txt with 10-step MCP workflow
- Rewrite subagent_system_prompt.txt with canonical server format,
  absolute rules, smoke-test procedures
- Remove mcp_servers mapping from config (no longer bound to
  external servers)

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

feat: admin API endpoints for individual MCP server CRUD ...

Add granular REST endpoints for managing single MCP servers:
- GET  /admin/mcp/config/{server_name}
- PUT  /admin/mcp/config/{server_name}
- DELETE /admin/mcp/config/{server_name}

Bulk endpoints remain for backward compatibility.

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

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>

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1

Rebuild dist for spinner overlay fix ...

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

Fix search spinner overlay on magnifying-glass icon ...

- Replace opacity-based hiding with display:none on .input-group-addon > i.
  Move spinner pseudo-element to nested &::after inside .input-group-addon
  with display:block + margin:auto for reliable centering.
- Tests pass (51/51)

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

Rebuild dist for search bug fixes ...

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

Fix search spinner overlay, scroller reset, highlight leak ...

- AppSidebar: use i.ph selector + !important for spinner overlay on
  input-group-addon icon. Add transition for smooth fade.
- SessionList: simplify DynamicScroller :key to 'search'/'all' only,
  removing sessions.length to prevent scroll reset on fetchMore.
- SessionList: pass empty searchQuery when searchActive is false,
  preventing stale highlights in normal session list.
- Tests pass (51/51)

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

Rebuild dist for final search UX polish ...

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

Final search UX polish: focus, cache, spinner opacity, scroller key ...

- AppSidebar: auto-focus input when search opens via querySelector.
  Spinner icon now hides via opacity:0 instead of visibility:hidden.
- SessionsStore: add searchCache ref + restoreSearch(). Cache stores last
  search results (items, hasMore, nextOffset) so reopening search avoids
  re-fetching when query hasn't changed.
- SessionList: add :key on DynamicScroller to force recreate when switching
  between search/normal mode, fixes pinned item spacing bug.
- Tests pass (51/51)

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

Rebuild dist for search UX fixes ...

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

Fix search spinner placement, msg-flash disappearance, results cleanup ...

- AppSidebar: spinner moved inside GnSearchField input-group-addon via CSS
  (:deep .input-group-addon overlay). Removed spinner from sessions-label.
- AppSidebar: closeSearch and handleSelect now call sessionsStore.exitSearch()
  and reload normal session list, so search results disappear after selection.
  toggleSearch restores previous query and re-activates search on reopen.
- CSS msg-flash: removed animation-fill-mode:both and background-color:transparent
  from keyframes, so message bubble keeps its original background after flash.
- SessionsStore: added exitSearch() method (preserves query, disables active flag).
- Tests pass (51/51)

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

Rebuild dist for search flash and highlight fixes ...

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

Fix search flash for assistant messages, move spinner, hide highlights ...

- MessageList: pass isFlashing prop to UserMessage/AssistantMessage instead
  of applying msg-flash on wrapper div. scrollToMessage now uses rawIndices
  to map backend match_index to grouped message index.
- UserMessage: add isFlashing prop, apply msg-flash to msg-user-bubble
- AssistantMessage: add isFlashing prop, apply msg-flash to msg-assistant-content
- ChatStore: add rawIndices to built messages (user, summary, assistant)
- AppSidebar: move spinner into sessions-label, remove from search field
- SessionList: accept searchOpen prop, pass empty searchQuery when closed
  so highlights disappear after selecting a session
- Tests pass (51/51)

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

Rebuild dist for search UX polish ...

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

Polish session search UX: GnSearchField, spinner, flash timing ...

- AppSidebar: use GnSearchField from gnexus-ui-kit, spinner during search,
  search toggle button always visible in sessions-header, hide search on select
- MessageList: fix msg-flash timing — make content visible before scrolling,
  extend flash duration to 2.5s with background + brightness
- CSS: enhance msg-flash keyframe animation
- Tests pass (51/51)

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

Rebuild dist for session search feature ...

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>

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1

Rebuild dist for tool card UX improvements ...

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

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1