It just says "Invalid Minecraft" if I follow the readme instructions and try to use it.
ln -s ~/.var/app/com.mojang.Minecraft/.minecraft/ ~/.minecraft
This command fixes it easily, in addition to the flatpak instruction given already in the README.
The fix here would be to search for ~/.var/app/com.mojang.Minecraft/.minecraft/ as the .minecraft folder if ~/.minecraft folder cannot be found or is invalid. Or just prompt the user to pick the right one, since both can be installed side-by-side.