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You missed `/bin/`, `/sbin/`, `/usr/bin/`, `/usr/sbin/` and the same in `/usr/local`. Luckily there are some efforts to clean this up: https://fedoraproject.org/wiki/Features/UsrMove

And ~/bin as well.

etc

I think I would actually be happy with a ~/etc. Dotfiles in the home directory needs to stop being a thing.