[[!comment format=mdwn username="http://joeyh.name/" ip="209.250.56.246" subject="comment 3" date="2013-11-15T17:48:42Z" content=""" Hmm. In your script, when you run `git annex sync` in a and then `echo aaaa > f`, f already exists at that point as a symlink. This actually ends up following the link and writing to .git/annex/objects. (fsck will detect that junk has been written there) That's a bug on its own; seems like direct mode is neglecting to lock down the .git/annex/objects directories to prevent writing to them like this. ---- However, this means that your script does not demonstrate the bug you originally reported. You remove b/f and sync, and since a/f has not been changed, the deleting is correctly synced to a, removing a/f. """]]