I don't know, better safe than sorry. You are touching users Data here. they should have an informed choice. A message box, something? maybe refuse to run, than he will notice.
So a first time newbie installs wine and is very happy with it. After 1/2 a year he feels more confident and the new release fixes a game he likes or something, He tries it out and his old setup is broken. Than what he think off wine? Unless we state it in bold letters in every possible documentation (and have a cancel flag like --noupgrade) than you must confirm with the user.
Wouldn't it be better to do good testing and have, ooh, I don't know, a beta testing program? In other words, to ensure we *don't* mangle the users data?
I'm not sure we should design this system on the assumption that we suck and will probably blow things up. I don't know of any other programs that use such a mechanism when upgrading!
thanks -mike