merge: use repo.wvfs.setflags() instead of util.setflags()
Most merge.py code goes through the vfs instead of maniulating
files directly, so let's do the same here.
Our full contribution guidelines are in our wiki, please see:
https://www.mercurial-scm.org/wiki/ContributingChanges
If you just want a checklist to follow, you can go straight to
https://www.mercurial-scm.org/wiki/ContributingChanges#Submission_checklist
If you can't run the entire testsuite for some reason (it can be
difficult on Windows), please at least run `contrib/check-code.py` on
any files you've modified and run `python contrib/check-commit` on any
commits you've made (for example, `python contrib/check-commit
273ce12ad8f1` will report some style violations on a very old commit).