This pull request introduces significant improvements to the configuration, documentation, and Docker setup for the Joern MCP server. The changes modernize the Docker image build process, provide a comprehensive example environment configuration, and overhaul the README.md to clarify features, installation, usage, and troubleshooting. The updates make the project more accessible and production-ready, with clearer instructions for both users and developers.

Configuration and Environment:

• Added a detailed .env.example file documenting server, Redis, Docker, session, CPG generation, query execution, storage, and optional GitHub settings, making environment-based configuration clearer and more robust.

Docker and Build Process:

• Replaced the old Dockerfile with a new, more robust Dockerfile.joern that uses the eclipse-temurin:21-jdk-jammy base image, installs all required dependencies, and ensures Joern CLI tools are installed and available in the container. [1] [2]
• Updated the build.sh script to build using Dockerfile.joern by default, aligning the build process with the new Dockerfile. [1] [2]

Documentation and Usage:

• Completely rewrote and expanded README.md:
  • Clarified features, supported languages, and architecture.
  • Provided step-by-step installation, setup, and configuration instructions.
  • Added explicit instructions for integrating with GitHub Copilot and using the MCP server with AI assistants.
  • Documented available tools, example usage, and common CPGQL queries.
  • Detailed troubleshooting steps for Docker, Redis, and server connectivity issues.
  • Updated development and contribution guidelines, project structure, and license section. [1] [2]

These changes collectively improve usability, maintainability, and onboarding for both users and contributors.