git annex sync - not pulling in files I haven't synced my git annex repositories for quite some time and was trying to synchronize them recently, but am getting an error which indicates I need to merge. I am getting the error: `Updates were rejected because a pushed branch tip is behind its remote counterpart.` I tried to run `git annex merge` and `git pull origin master`, but git complains that I need to run it in a work tree. [EDIT] I fixed that issue I believe, as my shell command was set to git-shell. Once I switched to git-annex-shell, it seemed to fix that issue. Now, I noticed that I have some files missing even after I have done a sync and a get. I added both repositories to the other so repository A has remote B and repository B has remote A. However, even after attempting to sync and get several times, I see no changes. Those files are still missing in one repository.

After playing around with it more, I had to reinitialize git and git annex. It appears to be working as expected now:

git init

git annex init

Once I did that, I could sync and it synced as expected.