[[!comment format=mdwn username="http://joeyh.name/" ip="108.236.230.124" subject="comment 1" date="2014-06-16T15:10:42Z" content=""" Reproduced this as described. Only happens when using the assistant in the second repository, which is a ssh remote of the first, and when there is not also a remote going the other way (so does not affect pairing). As I thought, the problem is that the master branch is not updated by the assistant when in direct mode, and while annex/direct/master is pulled by the other assistant, it does not merge it. """]]