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Why I dislike snaps
(lemmy.dbzer0.com)
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On the plus side, snaps also crap your system log full of petty little AppArmor events. And when snap gets its permissions wrong, you can easily fix it with SnapSeal.
(If Flatpak would just fucking stop rewriting every file path as /var/run/1000/blah, it would be the unquestionably superior package tech)
Friction between Snap and AppArmor is to be expected. The corporate sponsor of Snap, Canonical, is well known for their icy relationship with the corporate sponsor of AppArmor, Canonical.
If you don't want flatpaks to do that, you'll have to give them permission to see the entire file system
As another commentor pointed out, you can just use flatseal to give the app full access to whatever dirs you need.