Add comprehensive README for backend and fix core functionality issues

[Copilot]

This PR adds a comprehensive README.md file for the backend and resolves several critical configuration and startup issues that were preventing the application from running properly.

📚 Documentation Added

Created a detailed README.md covering:

• Project overview with clear feature status (implemented vs. planned)
• Complete project structure with explanations of each component
• Installation and setup guide with step-by-step instructions
• API endpoint documentation with working examples
• Configuration management explaining all environment variables
• Development guidelines and architecture overview

The documentation accurately reflects the current development status, making it clear which features are fully implemented, partially complete, or planned for future development.

🔧 Critical Fixes Applied

Configuration System

• Fixed get_base_dir() path resolution: Changed from Path(__file__).parent to Path(__file__).parent.parent to correctly point to the backend root directory
• Fixed directory creation order: Ensured parent directories are created before attempting to create database files
• Corrected YAML configuration paths: Changed absolute paths (/binaries, /models) to relative paths (binaries/, models/) to prevent permission errors

Database Integration

• Added missing get_session_manager() function: This singleton factory function was referenced throughout the codebase but not implemented
• Fixed database initialization: Resolved path resolution issues that were preventing SQLite database creation

Application Startup

• Added graceful LLM initialization: Server can now start without requiring model downloads for development/testing
• Added SKIP_DOWNLOADS environment variable: Allows running the server without downloading large model files
• Fixed import dependencies: Added missing os import in manager.py

✅ Verified Functionality

The following endpoints are now working and tested:

curl http://localhost:6750/api/health
# Returns: {"status":"ok","time":"2025-01-27T..."}

curl http://localhost:6750/api/version  
# Returns: {"app":"clyre-backend","version":"0.0.1"}

🚀 Impact

Before these changes, the backend could not start due to configuration errors. Now developers can:

1. Run the server immediately after following the README setup instructions
2. Test basic functionality without downloading large model files
3. Understand the project structure and contribute effectively
4. Deploy with confidence knowing the core infrastructure works

The README serves as both user documentation and a development roadmap, clearly communicating the project's current capabilities and future direction.

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