When modifying the backup logic in index.js in a way that changes the structure of the backup folder or the data stored per repository (e.g. new folders, renamed files, changed JSON shape), increment METADATA_VERSION at the top of index.js. This forces a full re-sync on the next run so all repositories are processed with the updated algorithm.
Keep README.md in sync with the actual backup scope implemented in index.js. Whenever what is backed up changes (e.g. new data types, folder structure, included/excluded files), update README.md to reflect the current state.