OSs need to stop letting applications have a free reign of all the files on the file system by default. Some apps come with apparmor/selinux profiles and firejail is also a solution. But the UX needs to change.
replies(5):
It's much like an Android application, except it can feel a little kludgy because not every application seems to realize it's sandboxed. If you click save, silent failure because it didn't have write access there isn't very user friendly.