# 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)
```bash
# 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
```bash
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

---

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