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>

config.py

@@ -1,20 +1,43 @@
 """
 Configuration and constants for Gemini MCP Server
+
+This module centralizes all configuration settings for the Gemini MCP Server.
+It defines model configurations, token limits, temperature defaults, and other
+constants used throughout the application.
+
+Configuration values can be overridden by environment variables where appropriate.
 """
 
 # Version and metadata
-__version__ = "2.8.0"
-__updated__ = "2025-09-09"
-__author__ = "Fahad Gilani"
+# These values are used in server responses and for tracking releases
+__version__ = "2.8.0"  # Semantic versioning: MAJOR.MINOR.PATCH
+__updated__ = "2025-09-09"  # Last update date in ISO format
+__author__ = "Fahad Gilani"  # Primary maintainer
 
 # Model configuration
-DEFAULT_MODEL = "gemini-2.5-pro-preview-06-05"
-THINKING_MODEL = (
-    "gemini-2.0-flash-thinking-exp"  # Enhanced reasoning model for think_deeper
-)
+# GEMINI_MODEL: The Gemini model used for all AI operations
+# This should be a stable, high-performance model suitable for code analysis
+GEMINI_MODEL = "gemini-2.5-pro-preview-06-05"
+
+# MAX_CONTEXT_TOKENS: Maximum number of tokens that can be included in a single request
+# This limit includes both the prompt and expected response
+# Gemini Pro models support up to 1M tokens, but practical usage should reserve
+# space for the model's response (typically 50K-100K tokens reserved)
 MAX_CONTEXT_TOKENS = 1_000_000  # 1M tokens for Gemini Pro
 
 # Temperature defaults for different tool types
+# Temperature controls the randomness/creativity of model responses
+# Lower values (0.0-0.3) produce more deterministic, focused responses
+# Higher values (0.7-1.0) produce more creative, varied responses
+
+# TEMPERATURE_ANALYTICAL: Used for tasks requiring precision and consistency
+# Ideal for code review, debugging, and error analysis where accuracy is critical
 TEMPERATURE_ANALYTICAL = 0.2  # For code review, debugging
+
+# TEMPERATURE_BALANCED: Middle ground for general conversations
+# Provides a good balance between consistency and helpful variety
 TEMPERATURE_BALANCED = 0.5  # For general chat
+
+# TEMPERATURE_CREATIVE: Higher temperature for exploratory tasks
+# Used when brainstorming, exploring alternatives, or architectural discussions
 TEMPERATURE_CREATIVE = 0.7  # For architecture, deep thinking