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@rysiek each of those locations in managed differently.

/usr/lib can be managed by individual packages, so they can add and delete things.

/etc/* packages can add things, but they can't delete them. They're allowed to be edited by the user and might not be upgradable. So effectively cruft builds up there.

/run/ is for runtime stuff probably configured by other services that shouldn't persist from one boot to the next.

This really isn't a systemd thing, but a result of Debian package policy.