As I tried to explain here: Every time I try to start annex, I have the problem that it wants to repair my repo. I'm not sure what's causing this and how to proceed. I would appreciate any pointers on how to triage the problem. There is a lot more info in the other thread.
OS X: 10.11.4 git: 2.8.3 (installed via brew) git annex: 6.20160527 (installed via brew)