On OS X 10.11.6, if you save any MS office file (.pptx, .docx, .xlsx) in a git-annex directory it won't be synced unless you restart the daemon. If you look in the logs it says "/Users/me/annex/test.pptx still has writers, not adding" This probably has something to do with temporary/lockfiles used by MS office apps. Any ideas on a workaround, other than restarting the daemon constantly?
A bug was opened about this: Git-annex and Microsoft Office files on OS X