docs: add security documentation and update repository branding

[herrschmidt]

Add Security Documentation and Update Repository Name

Changes

• Add comprehensive security documentation:
  • API key authentication setup and requirements
  • Rate limiting configuration and best practices
  • CORS protection settings
  • Production security recommendations
• Update repository name from doc-to-markdown to magic-markdown throughout all files
• Add environment variable setup instructions with examples
• Update backend configuration and dependencies

Files Changed

• README.md: Add security section and update repository name
• setup/README.md: Add environment setup instructions
• backend/app/config.py: Update configuration settings
• backend/requirements.txt: Update dependencies

Testing Checklist

• Documentation is clear and accurate
• All repository name references updated
• Environment variable examples are correct
• Security settings are properly documented
• Dependencies are up to date

Security Impact

This PR adds documentation for the security features we've implemented:

• API key authentication for all endpoints
• Rate limiting to prevent abuse
• CORS protection for trusted domains only