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.
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 “declutter” manually. Use your package manager.
The above is accurate, and can be considered accurate for any directory below or at well.
Per /run, it’s also mounted in memory, so trying to “declutter” it won’t get you anywhere and things will return on reboot.
So… you’re afraid of the command that does the thing you’re trying to do?