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>

.env.example

@@ -1,21 +1,28 @@
-# Example .env file for Gemini MCP Server
-# Copy this to .env and update with your actual values
+# Gemini MCP Server Environment Configuration
+# Copy this file to .env and fill in your values
 
-# Your Gemini API key (required)
-# Get one from: https://makersuite.google.com/app/apikey
-GEMINI_API_KEY=your-gemini-api-key-here
+# Required: Google Gemini API Key
+# Get your API key from: https://makersuite.google.com/app/apikey
+GEMINI_API_KEY=your_gemini_api_key_here
 
-# Docker-specific environment variables (optional)
-# These are set automatically by the Docker setup scripts
-# You typically don't need to set these manually
+# Optional: Redis connection URL for conversation memory
+# Defaults to redis://localhost:6379/0
+# For Docker: redis://redis:6379/0
+REDIS_URL=redis://localhost:6379/0
 
-# WORKSPACE_ROOT: Used for Docker path translation
-# Automatically set when using Docker wrapper scripts
-# Example: /Users/username/my-project (macOS/Linux)
-# Example: C:\Users\username\my-project (Windows)
-# WORKSPACE_ROOT=/path/to/your/project
+# Optional: Workspace root directory for file access
+# This should be the HOST path that contains all files Claude might reference
+# Defaults to $HOME for direct usage, auto-configured for Docker
+WORKSPACE_ROOT=/Users/your-username
 
-# MCP_PROJECT_ROOT: Restricts file access to a specific directory
-# If not set, defaults to user's home directory
-# Set this to limit file access to a specific project folder
-# MCP_PROJECT_ROOT=/path/to/allowed/directory
+# Optional: Logging level (DEBUG, INFO, WARNING, ERROR)
+# DEBUG: Shows detailed operational messages for troubleshooting
+# INFO: Shows general operational messages (default)
+# WARNING: Shows only warnings and errors
+# ERROR: Shows only errors
+LOG_LEVEL=INFO
+
+# Optional: Project root override for file sandboxing
+# If set, overrides the default sandbox directory
+# Use with caution - this controls which files the server can access
+# MCP_PROJECT_ROOT=/path/to/specific/project