I've gotten git-annex working as a smudge/clean filter today in the
smudge branch. It works ok in a local git repository.
git add lets
git-annex decide if it wants to annex a file's content, and checking out
branches and other git commands involving those files works pretty well.
It can sometimes be slow; git's smudge interface necessarily needs to copy the content of files around, particularly when checking out files, and so it's never going to be as fast as the good old git-annex symlink approach. Most of the slow parts are things that can't be done in direct mode repos though, like switching branches, so that isn't a regression.
No git-annex commands to manage the annexed content work yet. That will need a key to worktree file mapping to be maintained, and implementing that mapping and ensuring its always consistent is probably going to be the harder part of this.
Also there's the question of how to handle upgrades from direct mode repositories. This will be an upgrade from annex.version 5 to 6, and you won't want to do it until all computers that have clones of a repository have upgraded to git-annex 6.x, since older versions won't be able to work with the upgraded repository. So, the repository upgrade will need to be run manually initially, and it seems I'll need to keep supporting direct mode for v5 repos in a transition period, which will probably be measured in years.