Fix user tool execute() signature to accept ctx keyword argument ...

The tool_executor always passes ctx=ctx when calling tool.execute(),
but _try_module_level in loader.py created user tools with
_execute(self, params) only. This caused:

  Error: _execute() got an unexpected keyword argument 'ctx'

when calling get_current_datetime and any other module-level user tool.

- Add ctx=None parameter to the generated _execute wrapper
- Preserves backward compatibility with existing user tools

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>