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/run/user/1000: What to do with it?
(lemmy.ml)
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Don't "declutter" manually. Use your package manager.
I learned a lot in these comments but in this specific context:
These don't need decluttering I learned, but aren't managed by package managers either.
Flatpak is itself a file manager.
That duplicate of your folder in /run is due to filesystem links (or more likely a fuse mount, I've never actually looked into how flatpak works). But either way, they aren't copies of the data.
Don't use flatpak. It encourages dependency hell and ruins validation.
The search index isn't managed by you package manager, is it?