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Why is snaps hated
(lemmy.ml)
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Community icon by Alpár-Etele Méder, licensed under CC BY 3.0
To be fair, those are both issues with flatpak too. You can change the file system permissions with a command or flatseal, but I don't know of a fix for the password extension issue.
In general the integration of flatpak is quite good (even more if we compare it with snap), but there are still some gaps. In this case there are some solutions like this one.