Flatpak being securely sandboxed by default is both its biggest strength and its worst point of contention. The XDG is still scrambling to replicate the permission requests paradigm from Android on the Linux desktop.
csolisr
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Cake day: May 31st, 2025
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That reminds me, is Flatpak packaging CLI tools already?
I’d say you should check if any scheduled cleaning tasks are accidentally deleting your files.