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How about crud permission system
(lemmy.ml)
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Are you running on btrfs? If not, why not? If so, install snapper and grub-snap or refind-btrfs, or whatever, and go wild.
Sounds like you might also be missing backups, but snapper you can have run every 10 minutes at almost no overhead. Then it won't matter if you delete something; you can always grab it out of a snapshot.