I have the problem where in one repository I should not have any files anymore (according to git annex list --in .) but the annex directory still is very big (several GB). Git unused does not return any unused files so I guess they must be referenced somewhere. I do not use tags so it must be a branch. Could you tell me which of these branches are required by git annex and which are superfluous?

I have two repositories (at some point I had more): origin and exp and two special remotes (hubic and acd). exp is connected to hubic and acd.

on exp I have more space usage than indicated by git annex list exp has the following branches:

~/annex$ git branch -a
* master
  remotes/origin/HEAD -> origin/master

I have read the page on the internal workings and so far pretty much of all the wiki but if someone could point me to a description (if one exists) that explains which branch is used for what that would be great!

I understand that upon "git annex sync" a repo pulls the $REMOTE/master into remotes/$REMOTE/master and $REMOTE/synced/master into remotes/$REMOTE/synced/master. "git annex sync" on $REMOTE will push master to another repo into synced/master.

Cheers, Marek