[[!comment format=mdwn username="clement" subject="Details" date="2015-03-27T10:34:26Z" content=""" I tried it again with dfifferent usbs and filesystems, and it looks like it only happens with VFAT (e.g not ext). Retracing my step, here is what I do: 1. Create a repository on my local machine using git-annex assistant. 2. Create another non-bare repository on a VFAT usb stick and combine the two. 3. Add a file to the local repository 4. I doesn't synchronise and log shows the missing index error. It also happens the other way around. If I 1. Create a repository on the usb device, and 2. create a paired repository on my machine, I get a straight up Internal Server Error /mnt/USB/annexdir/.git/index: copyFile: does not exist (No such file or directory) """]]