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>

setup-docker.sh

@@ -43,6 +43,14 @@ REDIS_URL=redis://redis:6379/0
 # not just files within the current project directory. Additionally, Claude Code
 # could be running from multiple locations at the same time.
 WORKSPACE_ROOT=$HOME
+
+# Logging level (DEBUG, INFO, WARNING, ERROR)
+# DEBUG: Shows detailed operational messages, conversation threading, tool execution flow
+# INFO: Shows general operational messages (default)
+# WARNING: Shows only warnings and errors
+# ERROR: Shows only errors
+# Uncomment and change to DEBUG if you need detailed troubleshooting information
+LOG_LEVEL=INFO
 EOF
     echo "✅ Created .env file with Redis configuration"
     echo ""
@@ -168,6 +176,17 @@ echo "  }"
 echo "}"
 echo "==========================================="
 echo ""
+echo "===== CLAUDE CODE CLI CONFIGURATION ====="
+echo "# Add the MCP server via Claude Code CLI:"
+echo "claude mcp add gemini -s user -- docker exec -i gemini-mcp-server python server.py"
+echo ""
+echo "# List your MCP servers to verify:"
+echo "claude mcp list"
+echo ""
+echo "# Remove if needed:"
+echo "claude mcp remove gemini"
+echo "==========================================="
+echo ""
 
 echo "📁 Config file locations:"
 echo "  macOS: ~/Library/Application Support/Claude/claude_desktop_config.json"