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>

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>