I tried running "diff -u -r wine.ref wine". The problem is that this generated tons of diffs in files in the "CVS" directory. Don't ask me why there were differences there.
This is the right way, you just have to tweak the arguments to diff or grep away some stuff (CVS for example).
Use -x or -X options combined with grep [-v]
-x PAT --exclude=PAT Exclude files that match PAT. -X FILE --exclude-from=FILE Exclude files that match any pattern in FILE