refactor: cleanup and comprehensive documentation

Major changes:
- Add comprehensive documentation to all modules with detailed docstrings
- Remove unused THINKING_MODEL config (use single GEMINI_MODEL with thinking_mode param)
- Remove list_models functionality (simplified to single model configuration)
- Rename DEFAULT_MODEL to GEMINI_MODEL for clarity
- Remove unused python-dotenv dependency
- Fix missing pydantic in setup.py dependencies

Documentation improvements:
- Document security measures in file_utils.py (path validation, sandboxing)
- Add detailed comments to critical logic sections
- Document tool creation process in BaseTool
- Explain configuration values and their impact
- Add comprehensive function-level documentation

Code quality:
- Apply black formatting to all files
- Fix all ruff linting issues
- Update tests to match refactored code
- All 63 tests passing

🤖 Generated with [Claude Code](https://claude.ai/code)

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

setup.py

@@ -24,7 +24,7 @@ setup(
     install_requires=[
         "mcp>=1.0.0",
         "google-genai>=1.19.0",
-        "python-dotenv>=1.0.0",
+        "pydantic>=2.0.0",
     ],
     extras_require={
         "dev": [