I have this problem on my computers already, because configuration files and other program data is spewn across all kinds of directories and files all over the place.
The only two options I have is a) do a factory reset and reinstall software from scratch and spend time configuring things again, or b) live with all of the extra garbage that has been excreted by the software on my systems just so that I can keep the data that I actually want to keep.
Whereas to pick up all of my data that I do care about and copy only that and nothing extra to another place, is extremely time consuming to the point that it’s not realistically doable :(
Of course, cramming absolutely everything including user documents into the program won’t solve that either.
My ideal system would separate data that was written because of me (non-default config values, bookmarks, etc) from documents etc made by me, from garbage that the program wants to write that I absolutely do not care about and do not want to know about.