FILE_CLEANUP_SUMMARY.md

File Cleanup Summary

System Status

All core functionality is working. The cleanup preserves working files and archives documentation/test files.

Files Structure

✅ KEEP - Core System Files

├── app.py                          # Main Gradio application
├── main.py                         # Entry point
├── launch.py                       # Launch script
├── orchestrator_engine.py          # Orchestration logic
├── context_manager.py              # Context management
├── llm_router.py                  # LLM routing
├── models_config.py               # Model configuration
├── config.py                      # System configuration
├── requirements.txt                # Dependencies
├── install.sh                     # Installation script
├── quick_test.sh                  # Test script
├── database_schema.sql            # Database schema
├── Dockerfile.hf                   # Docker configuration
├── README.md                      # Main documentation
├── SYSTEM_FUNCTIONALITY_REVIEW.md # System status
└── KEEP_FILES.md                  # This file

src/
├── __init__.py
├── database.py
├── event_handlers.py
└── agents/
    ├── __init__.py
    ├── intent_agent.py
    ├── safety_agent.py
    └── synthesis_agent.py

📦 ARCHIVE - Documentation (40+ files)

Move to: archive/docs/

• All CONTEXT_*.md files (4 files)
• All SESSION_*.md files (3 files)
• All MOVING_WINDOW*.md files
• BUG_FIXES.md
• BUILD_READINESS.md
• DEPLOYMENT_*.md files (2)
• FINAL_FIXES_APPLIED.md
• GRACEFUL_DEGRADATION_GUARANTEE.md
• HF_TOKEN_SETUP.md
• IMPLEMENTATION_*.md files (2)
• INTEGRATION_*.md files (2)
• LLM_INTEGRATION_STATUS.md
• LOGGING_GUIDE.md
• PLACEHOLDER_REMOVAL_COMPLETE.md
• SYSTEM_UPGRADE_CONFIRMATION.md
• TECHNICAL_REVIEW.md
• WORKFLOW_INTEGRATION_GUARANTEE.md
• FILE_STRUCTURE.md
• AGENTS_COMPLETE.md
• COMPATIBILITY.md

📦 ARCHIVE - Duplicates (Entire directory)

Move to: archive/duplicates/

• Research_AI_Assistant/ (entire directory - duplicate of main files)

📦 ARCHIVE - Test/Development Files

Move to: archive/test/

• acceptance_testing.py
• agent_protocols.py
• agent_stubs.py
• cache_implementation.py
• faiss_manager.py
• intent_protocols.py
• intent_recognition.py
• mobile_components.py
• mobile_events.py
• mobile_handlers.py
• performance_optimizations.py
• pwa_features.py
• test_setup.py
• verify_no_downgrade.py

Commands to Execute

Option 1: Manual Archive (Recommended)

# Create archive directories
mkdir -p archive/docs archive/duplicates archive/test

# Move documentation files
mv CONTEXT_*.md SESSION_*.md MOVING_WINDOW*.md archive/docs/
mv BUG_FIXES.md BUILD_READINESS.md DEPLOYMENT*.md archive/docs/
mv FINAL_FIXES*.md GRACEFUL*.md IMPLEMENTATION*.md archive/docs/
mv INTEGRATION*.md LLM*.md LOGGING*.md PLACEHOLDER*.md archive/docs/
mv SYSTEM_UPGRADE*.md TECHNICAL*.md WORKFLOW*.md archive/docs/
mv FILE_STRUCTURE.md AGENTS_COMPLETE.md COMPATIBILITY.md archive/docs/

# Move test files
mv acceptance_testing.py agent_*.py cache_implementation.py archive/test/
mv faiss_manager.py intent_*.py mobile_*.py archive/test/
mv performance_*.py pwa_features.py test_*.py verify_*.py archive/test/

# Move duplicates
mv Research_AI_Assistant archive/duplicates/

Option 2: Python Script

python cleanup_files.py

Result

After cleanup:

• Root directory: 16 core system files
• src/: 4 Python files
• Total: ~20 files (clean, organized)
• archive/: 60+ archived files

Benefits

1. ✅ Clean workspace - Easy to navigate
2. ✅ Clear structure - Only essential files visible
3. ✅ Preserved history - All docs in archive
4. ✅ No functional changes - System still works
5. ✅ Easy maintenance - Clear separation

Next Steps

1. Run cleanup script or manual commands
2. Verify system still works: python app.py
3. Update .gitignore to ignore archive/
4. Commit changes

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Status: Ready to execute cleanup
Risk: Low (all files preserved in archive)
Benefit: High (clean, organized codebase)