I simply use a 'checkout' process where all website assets to be deployed are copied into for example a /dst folder and the folder then rsync'd to the webroot (

I simply use a 'checkout' process where all website assets to be deployed are copied into for example a /dst folder and the folder then rsync'd to the webroot (with rsync -ru --delete --chmod). This avoids clutter and still allows to just update changed files. The actual page source is still under git.