So… you’re afraid of the command that does the thing you’re trying to do?

I’m surprised no one’s mentioned the security implications. Mounting with nosuid and nodev options can undermine rootkit or privileged escalation exploits.

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.

You’re going to want to look up things like symlinks, hard links, fuse filesystems, and bind mounts among other concepts. Your “whole directory” and other duplicates are artifacts of how the filesystem and process management works, and simply running fsearch or find over them is going to be confusing if you don’t know what you’re looking at.

One Unix concept that carries over to Linux is that everything is a file. Your shared memory space, process data, device driver interfaces, etc, all of it is accessible somewhere in the same virtual filesystem tree as the actual files.

Because of this, there’s very little reason to have the whole filesystem indexed from root. If you’re worried about space usage, you want to work with packages through the package manager. If you’re worried about system integrity, you’ll want package validators.

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.

I actually want to learn enough code to contribute, but there’s this gap between “how to code” and “how to participate in a modern software project”.

Like, I’ve created plenty of little things. Discord bots, automation scripts, plenty of sysadmin stuff for work, etc. But like, I clone a git repo cause there’s a home assistant bug I’d like to fix for example, and I’m immediately lost on where to start.

I’d imagine tar is included with the install media.

I could be wrong, but isn’t the entire debian stable tree maintained for years via open source contributions? Sure the redhat downstreams might be on their own, but there’s plenty of non-commercial distros that keep up to date.