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I've now fixed the worst problem with v6 mode, which was that get/drop of
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unlocked files would cause git to think that the files were modified.
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Since the clean filter now runs quite fast, I was able to fix that by,
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after git-annex updates the worktree, restaging the not-really-modified 
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file in the index.
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This approach is not optimal; index file updates have overhead; and only
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one process can update the index file at one time. [[todo/smudge]] has a
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bunch of new todo items for cases where this change causes problems. Still,
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it seems a lot better than the old behavior, which made v6 mode nearly
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unusable IMHO.
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This work is supported by the NSF-funded DataLad project.
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