I've now fixed the worst problem with v6 mode, which was that get/drop of unlocked files would cause git to think that the files were modified.

Since the clean filter now runs quite fast, I was able to fix that by, after git-annex updates the worktree, restaging the not-really-modified file in the index.

This approach is not optimal; index file updates have overhead; and only one process can update the index file at one time. smudge has a bunch of new todo items for cases where this change causes problems. Still, it seems a lot better than the old behavior, which made v6 mode nearly unusable IMHO.

This work is supported by the NSF-funded DataLad project.