Fix test_rejects_empty to match current _check_path behavior ...

Empty string is explicitly rejected by _check_path since the
guard clause was added. The test comment was stale.

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

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>

Improve content publishing UX

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>