# Files to Keep - System Functionality

## Core System Files (Keep)

### Main Application
- `app.py` - Main Gradio application
- `main.py` - Entry point
- `orchestrator_engine.py` - Main orchestration
- `context_manager.py` - Context management
- `llm_router.py` - LLM routing
- `models_config.py` - Model configuration
- `config.py` - System configuration

### Source Code (`src/`)
- `src/` directory (all files)
  - `src/agents/` - All agent implementations
  - `src/database.py` - Database management
  - `src/event_handlers.py` - Event handling

### Supporting Files
- `requirements.txt` - Python dependencies
- `README.md` - Main documentation
- `install.sh` - Installation script
- `quick_test.sh` - Quick test script
- `database_schema.sql` - Database schema

## Documentation Files (Keep ONLY Essential)

### Essential Documentation
- `README.md` - Main project documentation
- `SYSTEM_FUNCTIONALITY_REVIEW.md` - Current system status
- `SESSION_UI_FIX_COMPLETE.md` - UI fixes documentation

### Archive (Move to archive/docs/)
- `CONTEXT_MEMORY_FIX.md`
- `CONTEXT_SUMMARIZATION_ENHANCED.md`
- `CONTEXT_SUMMARIZATION_IMPLEMENTED.md`
- `CONTEXT_WINDOW_INCREASED.md`
- `SESSION_CONTEXT_FIX.md`
- `SESSION_CONTEXT_FIX_SUMMARY.md`
- All other `*.md` files in root and Research_AI_Assistant

## Research_AI_Assistant (Archive Entire Directory)

All files in `Research_AI_Assistant/` are duplicates and should be archived.

## Test Files (Move to archive/test/)
- `acceptance_testing.py`
- `test_setup.py`
- `verify_no_downgrade.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`

## Files to Archive

### Documentation (Keep only 3 essential docs)
Archive all markdown files except:
- `README.md`
- `SYSTEM_FUNCTIONALITY_REVIEW.md`
- `SESSION_UI_FIX_COMPLETE.md`

### Research_AI_Assistant (Full duplicate)
- Entire `Research_AI_Assistant/` directory

### Test/Development Files
- All `*_test.py`, `agent_stubs.py`, protocol files
- Mobile-specific files (not using mobile UI currently)
- Optimization/performance files (optional enhancements)

## Summary

**Keep**: Core system files + 3 essential docs  
**Archive**: 40+ documentation files + Research_AI_Assistant directory + test files