Let's say your daily system is going through some "big changes", like changing from a X11 DE to a Wayland Compositor, or you stop using an application with a lot of configuration and dependencies. How do you proceed to "clean up" after the change? Or do you simply go for a fresh install?

I personally don't to much outside of uninstalling a package along with dependencies and checking for orphaned packages, so I'm curious to know if there are some more elaborate and efficient cleaning routines out there.

I've also read someone claim that some software like DEs install some hacks directly to the kernel so cleaning up after an uninstall would be rather hard. I don't really get what that's about, can anyone also comment on that?