# Project Cleanup Summary - December 4, 2025

## Overview
Comprehensive project cleanup and reorganization to improve maintainability and follow best practices.

## Changes Completed

### 1. Test Files Organization
**Location**: `tests/manual/`

Moved 11 test files from root directory to proper test location:
- `test_cli_integration.py`
- `test_file_scan_ewtn.py`
- `test_final_comprehensive.py`
- `test_full_index_ewtn.py`
- `test_gitignore_ewtn.py`
- `test_root_detection_direct.py`
- `test_visualization.py`
- `test_visualizer_detailed.py`
- `test_visualizer_line_by_line.py`
- `test_visualizer.py`
- `test_with_cdp.py`
- `debug_visualizer.py`

### 2. Documentation Organization
**Location**: `docs/summaries/`

Moved 7 summary documentation files:
- `DOCUMENTATION_REORGANIZATION_COMPLETE.md`
- `HOMEBREW_INTEGRATION_SUMMARY.md`
- `HOMEBREW_INTEGRATION_USAGE.md`
- `HOMEBREW_TAP_UPDATE_STATUS.md`
- `HOMEBREW_TAP_UPDATE_SUMMARY.md`
- `HOMEBREW_TEST_RESULTS.md`
- `PERFORMANCE_OPTIMIZATION_SUMMARY.md`

**Location**: `docs/research/`

Moved visualization test artifacts:
- `test_page.html`
- `visualization_test_report.md`

### 3. Large Data Files
**Location**: `.mcp-vector-search/visualization/`

Relocated large data file:
- `chunk-graph.json` (29MB) → proper visualization directory

### 4. Temporary Artifacts Cleanup
Removed build artifacts and caches:
- `.mypy_cache/` directory
- `htmlcov/` directory
- `coverage.xml` file

### 5. Process Cleanup
Killed all running background visualization servers on ports 8080-8090

### 6. Code Quality Improvements

#### Fixed Linting Issues:
- **Ruff E741**: Changed ambiguous variable name `l` to `link` in `visualize.py`
- **Bandit B403/B301**: Added security suppressions for trusted pickle files with proper comments

#### Pre-commit Hooks Passed:
- ✅ Trailing whitespace check
- ✅ End of files check
- ✅ Large files check
- ✅ Merge conflicts check
- ✅ Debug statements check
- ✅ Black formatting
- ✅ Ruff linting
- ✅ Ruff format
- ✅ Mypy type checking
- ✅ Bandit security scan

## Project Structure After Cleanup

```
mcp-vector-search/
├── src/                      # Source code (clean)
├── tests/
│   └── manual/              # All test files properly organized
├── docs/
│   ├── research/            # Test artifacts and research notes
│   └── summaries/           # Project summary documents
├── .mcp-vector-search/
│   └── visualization/       # Visualization data and artifacts
├── scripts/                 # Build and utility scripts
└── [project root]          # Clean, essential files only
```

## Benefits

1. **Improved Organization**: All files in appropriate directories by type and purpose
2. **Cleaner Root**: No loose test or temporary files in project root
3. **Better Maintainability**: Clear separation of concerns
4. **Code Quality**: All linting and security checks passing
5. **Git History**: Clean commit with comprehensive documentation

## Git Commit
- **Commit**: `cd9a454`
- **Message**: "chore: comprehensive project cleanup and organization"
- **Files Changed**: 11 files
- **Lines Added**: +1120, -65
- **Pre-commit**: All hooks passed ✅

## Verification

### Root Directory Status
```bash
$ ls -1 *.py *.html *.json 2>/dev/null
# No loose files remaining ✓
```

### Git Status
```bash
$ git status
On branch main
Your branch is ahead of 'origin/main' by 1 commit.
nothing to commit, working tree clean ✓
```

### Running Servers
```bash
$ lsof -i :8080-8090
# No visualization servers running ✓
```

## Next Steps

1. Push changes to remote repository
2. Consider creating a comprehensive `.editorconfig` for consistent formatting
3. Document the new organization structure in main README if needed
4. Update any CI/CD scripts that reference old file locations

## Notes

- The `.gitignore` already had proper patterns for test files and large data files
- All changes follow existing project conventions
- Pre-commit hooks ensure code quality standards are maintained
- Security suppressions for pickle files are properly documented with reasoning

---
*Cleanup completed: December 4, 2025*
*Generated during project cleanup session*
