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/run/user/1000: What to do with it?
(lemmy.ml)
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Don't delete it. It's an area of the filesystem where the current user session data is kept. This includes things like sockets to communicate with other session components and lock files. It's usually hosted on a ram disk so takes up no space in the system and goes away when you shutdown your machine.
Or it comes back the same way but doesn't pose a problem either?
Files in /run will be (re)created (and removed) at runtime if/when needed by programs that need them. They pose no problems and don't persist between reboots.