Backup flatpak apps as well
Lots of apps are easier to install as flatpaks, so it'd be nice to backup those as well. This link and this link provide some details on how to backup the app list and user data. It sounds like the config and user data should already be getting backed up if the home directory is getting backed up, and then backing up repos and apps can be done through processing flatpak remotes --show-details
and flatpak list --app --show-details