Flatpak is another way of installing apps onto Linux or something.
The default installation will install for all users and probably put stuff onto the root partition. If this is not what you want, then install for your current user, using:
flatpak --user install flathub io.atom.Atom
Keeping tabs on size
A bunch of files are created in
/var/lib/flatpak (in the default installation):
Flatpak uses OSTree to distribute and manage applications and runtimes. The repo/ in the above tree is the local OSTree repository.
To uninstall all unused packages:
flatpak uninstall --unused