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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.
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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.
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