Cleanup the repo

I think we don't need the marked <-- files/directories anymore.

.
├── deploy <--
├── deploy.py <--
├── images
├── LICENSE
├── pyproject.toml
├── README.md
├── requirements.txt <-- update
├── toolMetrics <--
├── tools.json 
└── update_metrics.py

Mainly the deploy.py and it's directory and the tool metrics directory.