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>

tests/test_config.py

@@ -3,7 +3,7 @@ Tests for configuration
 """
 
 from config import (
-    DEFAULT_MODEL,
+    GEMINI_MODEL,
     MAX_CONTEXT_TOKENS,
     TEMPERATURE_ANALYTICAL,
     TEMPERATURE_BALANCED,
@@ -31,7 +31,7 @@ class TestConfig:
 
     def test_model_config(self):
         """Test model configuration"""
-        assert DEFAULT_MODEL == "gemini-2.5-pro-preview-06-05"
+        assert GEMINI_MODEL == "gemini-2.5-pro-preview-06-05"
         assert MAX_CONTEXT_TOKENS == 1_000_000
 
     def test_temperature_defaults(self):