I\'ve read all of the similar questions on this; it seems that none of the following have worked:
Delete offending files git reset --hard HEAD git stash git
Solved, using the following command set:
git reset --hard git pull --rebase git rebase --skip git pull
The trick is to rebase the changes... We had some trouble rebasing one trivial commit, and so we simply skipped it using git rebase --skip (after having copied the files).