# Root Folder Cleanup Summary

This document summarizes the organization of files from the root directory into appropriate subfolders.

## Files Moved

### Documentation Files → `docs/`
- `DEPLOYMENT.md` → `docs/deployment/`
- `DOCKER_COMPLETE.md` → `docs/deployment/`
- `DOCKER_GUIDE.md` → `docs/deployment/`
- `ENHANCED_TRAINING_SUMMARY.md` → `docs/status/`
- `IMPLEMENTATION_COMPLETE.md` → `docs/status/`
- `INSTALLATION_FIX.md` → `docs/status/`
- `MONAI_IMPLEMENTATION_STATUS.md` → `docs/status/`
- `MONAI_TESTS_COMPLETE.md` → `docs/status/`
- `ROOT_ORGANIZATION_COMPLETE.md` → `docs/status/`
- `VERIFICATION_STATUS.md` → `docs/status/`
- `VERIFICATION_SUCCESS.md` → `docs/status/`

### Setup Scripts → `scripts/setup/`
- `setup_fixed.sh` → `scripts/setup/`
- `cleanup_root.sh` → `scripts/setup/`
- `organize_root.sh` → `scripts/setup/`
- `move_files.sh` → `scripts/setup/`

### Demo Scripts → `scripts/demo/`
- `demo_complete_workflow.sh` → `scripts/demo/`
- `demo_enhanced_workflow.sh` → `scripts/demo/`

### Validation Scripts → `scripts/validation/`
- `validate_docker.py` → `scripts/validation/`
- `validate_monai_integration.py` → `scripts/validation/`
- `verify_monai_checklist.py` → `scripts/validation/`
- `verify_monai_venv.sh` → `scripts/validation/`
- `test_docker.sh` → `scripts/validation/`
- `test_enhanced_inference.py` → `scripts/validation/`
- `test_imports_quick.py` → `scripts/validation/`
- `test_monai_imports.py` → `scripts/validation/`
- `test_overlay_quality.py` → `scripts/validation/`
- `test_overlay_system.py` → `scripts/validation/`
- `test_system.py` → `scripts/validation/`
- `test_viz_system.py` → `scripts/validation/`
- `debug_datalist.py` → `scripts/validation/`

### Development Config → `config/development/`
- `requirements-docker.txt` → `config/development/`
- `requirements-fixed.txt` → `config/development/`
- `mypy.ini` → `config/development/`
- `pytest.ini` → `config/development/`
- `.ruff.toml` → `config/development/`

## Files Kept in Root
- `run.sh` (main entry point)
- `README.md` (project documentation)
- `LICENSE` (license file)
- `requirements.txt` (main requirements)
- `setup.py` (package setup)
- `config.json` (main configuration)
- `.env` files moved to `docker/` and are no longer kept in the repo root

## Updated References
- All scripts and configuration files updated to reference new file locations
- GitHub workflows updated for moved config files
- Docker files updated for moved requirements
- README.md updated with new paths
- Python imports updated where necessary

## Benefits
- ✅ Cleaner root directory with only essential files
- ✅ Logical organization by file type and purpose
- ✅ Easier navigation and maintenance
- ✅ All functionality preserved with updated references
- ✅ Better project structure for development and deployment
