Proper package management is the only solution... I still manage to screw up and forget a checkbox here or there once in a while and next thing you know, I spend half an hour cleaning it up.

Well, it seems to be the way Microsoft wants to go at it anyway what with the atrocious Windows store.

As a sidenote, I really wish we'd get generic package management. A proper package management server and protocol that is. Something that can be used and picked up by Windows and linux distros but also by domain-specific packages (pypi, etc), browser extensions, games with addon repositories and so on.

It's sad that right now we can't answer "and now we need package management" by "sure, let me fire up pkgserve.d" or something.