[[!comment format=mdwn username="http://joeyh.name/" ip="209.250.56.35" subject="comment 1" date="2014-01-06T16:02:45Z" content=""" I'm not seeing data loss. It looks like the contents of your files are still there, you just need to rename them back to the right directory names. If you're using indirect mode, you should be able to do this: mv .git/annex/objects . chmod -R u+w objects git annex add objects That will re-inject all the file contents with the right names. You can then delete the objects directory, which should only contain symlinks at that point. ---- Moving git-annex to using lower case hash directories is on the very long term todo list, due to various crappy filesystems (problems mostly worked around by direct mode). Since it requires changing every symlink in every existing git-annex repository, which will be extremely disruptive, I'd need a much better reason than dropbox to do it now. I have no interest, in general, in making git-annex use filenames that meet whatever limitations dropbox wants to impose on its users. """]]