The Krita VCS plugin (aka Krita VC)
A small Version Control panel that lives right inside Krita, so you can save a version, set work aside, or switch branches without ever leaving your canvas. It runs on the exact same engine and the exact same history as the desktop app. Save from either one, and the other sees it.
Download the plugin← Krita plugin
Picking exactly what goes in
Every file in the list has a checkbox, ticked by default. Untick anything you'd rather leave out, and Commit, Checkpoint, Discard, and Set aside will only act on the ticked files.