fix: critical conversation history bug and improve Docker integration

This commit addresses several critical issues and improvements:

🔧 Critical Fixes:
- Fixed conversation history not being included when using continuation_id in AI-to-AI conversations
- Fixed test mock targeting issues preventing proper conversation memory validation
- Fixed Docker debug logging functionality with Gemini tools

🐛 Bug Fixes:
- Docker compose configuration for proper container command execution
- Test mock import targeting from utils.conversation_memory.* to tools.base.*
- Version bump to 3.1.0 reflecting significant improvements

🚀 Improvements:
- Enhanced Docker environment configuration with comprehensive logging setup
- Added cross-tool continuation documentation and examples in README
- Improved error handling and validation across all tools
- Better logging configuration with LOG_LEVEL environment variable support
- Enhanced conversation memory system documentation

🧪 Testing:
- Added comprehensive conversation history bug fix tests
- Added cross-tool continuation functionality tests
- All 132 tests now pass with proper conversation history validation
- Improved test coverage for AI-to-AI conversation threading

✨ Code Quality:
- Applied black, isort, and ruff formatting across entire codebase
- Enhanced inline documentation for conversation memory system
- Cleaned up temporary files and improved repository hygiene
- Better test descriptions and coverage for critical functionality

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

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

server.py

@@ -47,8 +47,22 @@ from tools import (
 )
 
 # Configure logging for server operations
-# Set to DEBUG level to capture detailed operational messages for troubleshooting
-logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+# Can be controlled via LOG_LEVEL environment variable (DEBUG, INFO, WARNING, ERROR)
+log_level = os.getenv("LOG_LEVEL", "INFO").upper()
+
+# Configure both console and file logging
+log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+logging.basicConfig(level=getattr(logging, log_level, logging.INFO), format=log_format)
+
+# Add file handler for Docker log monitoring
+try:
+    file_handler = logging.FileHandler("/tmp/mcp_server.log")
+    file_handler.setLevel(getattr(logging, log_level, logging.INFO))
+    file_handler.setFormatter(logging.Formatter(log_format))
+    logging.getLogger().addHandler(file_handler)
+except Exception as e:
+    print(f"Warning: Could not set up file logging: {e}")
+
 logger = logging.getLogger(__name__)
 
 # Create the MCP server instance with a unique name identifier