I recently cleaned my git history using:

git filter-branch --tree-filter 'rm -rf personal/Mail' --prune-empty HEAD
git for-each-ref --format="%(refname)" refs/original/ | xargs -n 1 git update-ref -d
git gc

I then ran:

git annex unused

But was surprised to find that it didn't report any unused files. Not surprisingly (given that I didn't touch the annex data at all so far), when looking into .git/annex/objects/ I still find the content of all the files that are now not used anymore.

Is there a way to clean these up besides creating a fresh clone of the repository?