Of course I was speaking in the stated context of someone just managing their files, not a modder. A modder will want to keep their backup files, but they're useless to the audience.
That's what I am so far, a simple user. I made 2 backup archives, one with the retail install which is free of any modification whatsoever, the second one with all the mods I downloaded and installed properly, I mean with good mod.ini file where it lacked one. And that's when I saw lots of files like cache files and .bak and .00x files which are backup files I didn't create myself, I would have never let these files in a publicly released archive so I removed them. But I understand it's good not to remove files created in the 'cache' folders.
I don't mind losing mission files as I always reset campaigns, however I do care about player files! anyway the progress one makes are stored in the player file, not in any mission file aren't they?
I'm only doing it so that I can have a very clean directory tree should something go wrong with my install that would require me to start over with a fresh one... OK this feels kind of maniac.

A+
Jack H.