running 'git annex sync' doesn't merge the branches as expected (from the limited testing I have done) with git 1.7.10, the behaviour of merge has changed, it now asks for a commit message. I would expect setting GIT_MERGE_AUTOEDIT=no should resolve this issue.
I had to manually do a merge (or set that variable) to get the branches back in sync again, this confused me a bit when git-annex watch was running in the background on a remote and it did not pick up the changes.
Yeah, I tend to miss these since the first thing I did when this misfeature was being posted was to write a mail discouraging them from doing it (sadly ignored), and then set in ~/.environment:
# My time is more valuable than git's new, bad default
GIT_MERGE_AUTOEDIT=no
export GIT_MERGE_AUTOEDIT
Anyway, I've made sync run merge with --no-edit now. done --Joey