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>

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>

Allow subagents to use selected profiles

Improve 3D modeling validation prompts

Add artifact source previews

Improve content publishing UX

Complete phase 7 regression test coverage

Add regression tests for content publishing and LLM timeouts

Clarify share file publishing boundaries

Add 62 tests across all planned phases + fix integration flakiness ...

- Phase 3: 19 API route integration tests (health, agents, sessions, messages)
- Phase 3: 7 WebSocket integration tests (connect, send, replay, invalid, stop)
- Phase 4: 9 agent tests (_check_context_size, _iter_stream_guarded)
- Phase 4: 5 planning tests (_parse_plan_steps)
- Phase 5: 22 tool tests (filesystem 13, code_exec 5, terminal 4)
- Fix flaky integration tests by patching module-level singletons
  (_session_store, _registries, _workers) instead of getter functions,
  because FastAPI Depends() captures the original function at import time.
- Update docs/testing.md coverage table (150 total tests)

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