Version control filesystem for software packages and system configuration

Inspired by the uninstallable Windows Genuine Advantage (gotta love how Microsoft's bad ideas inspire good ideas in revolt) it's clear that some parts of an operating system filesystem, namely the installed software packages and system configuration, should act like as if in a version control system, so that you can always go back and see who did what, when, and possibly why, and always be able to undo changes. One can discover and recover from trojans. One can save disk space such that when an old version of a file is overwritten, but that file came from a package, one only needs to maintain a pointer to the package from where to restore the file if it is ever needed. The pointer may even be to the internet or some DHT, but trusted.