[[!comment format=mdwn username="joey" subject="""comment 2""" date="2015-04-29T17:18:17Z" content=""" --clean-duplicates is not really intended to go do a full verification that the annexed content is present. I can see how this is surprising; it would probably be better if it were named "--clean-seen-content" or something like that. But, --deduplicate has the same behavior for such files, and I can't see a way to rename that more effectively. For now I have improved the git-annex-import man page to note that annexed content that's been removed would make a file be considered a duplicate. """]]