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Borg Backup. It can work locally or over network. Takes snapshots of the files you give it. Performs deduplication, compression and optionally encryption. You can check the integrity of the backups and repair them. There’s a very simple to use GUI for it called Pika Backup to get you started.
The problem is that the main container can (and usually does) rely on other layers, and you may need to pull updates for those too. Updating one app can take 5-10 individual pulls.