# File Consolidation Summary
## Date: December 6, 2025
### Overview
Successfully consolidated root directory files from ~250 files to 59 items (files and directories).
### Actions Taken
#### 1. Created Directory Structure
- `tests/root_tests/` - For test files from root
- `examples/` - For demo and example scripts
- `scripts/utilities/` - For utility scripts
- `docs/implementation/` - For implementation summaries
- `docker/dockerfiles/` - For Docker files
- `config/templates/` - For environment templates
- `.metadata/` - For metadata files
#### 2. Moved Test Files (91 files)
- Moved all `test_*.py` files to `tests/root_tests/`
- Moved test runner scripts: `run_document_tests.py`, `run_parallel_tests.py`, `run_reranking_tests.py`
#### 3. Moved Demo/Example Scripts (23 files)
- Moved all `demo_*.py` files to `examples/`
- Moved `example_*.py` files to `examples/`
- Moved `java_plugin_demo.py` and `swift_demo.swift` to `examples/`
#### 4. Moved Utility Scripts (29 files)
- Moved indexing scripts: `index_*.py`, `populate_bm25_*.py`, `create_*.py`
- Moved analysis scripts: `analyze_gitignore_security.py`, `benchmark_reranking_comparison.py`
- Moved debug scripts: `debug_*.py`
- Moved verification scripts: `verify_*.py`
- All moved to `scripts/utilities/`
#### 5. Moved Implementation Summaries (22 files)
- Moved all `*_IMPLEMENTATION*.md`, `*_SUMMARY.md`, `*_REPORT*.md`, `*_PLAN*.md`, `*_RESULTS*.md` files to `docs/implementation/`
#### 6. Moved Docker Files (5 files)
- Moved `Dockerfile` and all `Dockerfile.*` variants to `docker/dockerfiles/`
- Kept docker-compose files in root for easier access
#### 7. Moved Database Files (3 files)
- Moved `code_index.db`, `code_index_backup.db`, `code_index_original.db` to `data/`
#### 8. Moved Log Files (9 files)
- Moved all `.log` and log-related `.txt` files to `logs/`
#### 9. Deleted Artifact Files (7 files)
- Removed unusual empty files: `B[Run`, `C[Review`, `D{Issues`, `G[Review`, `H[AI`, `No`, `Yes`
#### 10. Consolidated Environment Templates
- Moved `.env.production.example`, `.env.production.template`, `.env.staging.template` to `config/templates/`
- Kept `.env.example` in root as the primary template
#### 11. Moved Verification/Analysis Docs
- Moved `mcp_verification_*.md`, `test_claude_session_analysis.md`, `mock_usage_analysis.md` to `docs/reports/`
- Moved `mcp_test_*.md` templates to `docs/reports/`
#### 12. Additional Organization
- Moved JSON report files to `docs/reports/`
- Moved `index-archive.tar.gz` to `data/`
- Created `.metadata/` directory and moved metadata files there
- Moved documentation files like `MARKDOWN_INDEX.md` to `docs/`
### Files Kept in Root (Essential Only)
- **Core Documentation**: README.md, LICENSE, CHANGELOG.md, CONTRIBUTING.md, CODE_OF_CONDUCT.md, SECURITY.md, TROUBLESHOOTING.md, ROADMAP.md
- **Essential Configuration**: .gitignore, pyproject.toml, requirements.txt, requirements-production.txt, Makefile, pytest.ini, tox.ini
- **Docker Compose Files**: All docker-compose*.yml files
- **Main Scripts**: dev.sh, docker-setup.sh, codex-setup.sh, scaffold_mcp.sh, setup-documentation.sh
- **Agent Instructions**: AGENTS.md, CLAUDE.md
- **MCP Configuration**: .mcp.json, .mcp-index.json, .mcp-index-ignore
- **CLI Files**: mcp_cli.py, mcp_server_cli.py
- **Other Config**: plugins.yaml, prometheus.yml, package-lock.json
### Result
The root directory is now much cleaner and more organized, with files logically grouped into appropriate directories. This makes the project structure easier to navigate and maintain.
