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?
