I created a local annex directory that's an adjusted branch used with the assistant. On another machine, I initialized an annex directory, then made this into a full-backup ssh remote for my local.

After the assistant pushes to the remote, and the remote runs `git annex sync`, the remote is missing some directories and has some extra directories. For example, it has the extra directory `Documents/programs/Documents/programs/`, which has different contents than `Documents/programs/`. Both directories are missing the subdirectory `graphing_experiments/`.

From my local, `git annex whereis Documents/programs/graphing_experiments` says the directory exists on the remote. But it's not there.

I recreated the remote from scratch and the problem persists.

The assistant says the remote is caught up, and is keeping up with new content changes. What could cause this?