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 developer profile; replace write_tool pattern with direct filesystem approach ...

- New TestToolTool: runs a user tool's execute() from disk in isolation,
  returns result or full traceback. No stale module cache — always fresh import.
- New developer profile: full architecture knowledge in system prompt
  (format rules, file locations, workflow, data persistence, common mistakes),
  test_tool + reload_tools + filesystem/terminal/code_exec toolset, spawn_agent
  for API research only.
- Remove write_tool and reload_tools from server_admin and smart_home profiles.
- persona.txt: drop SELF-EXTENSION block; add one-liner to switch to developer
  profile when the user asks to create/edit a tool.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>