[[!comment format=mdwn username="http://joeyh.name/" nickname="joey" subject="comment 1" date="2013-05-31T21:17:17Z" content=""" More generally, symbolic links cannot have permissions of their own, and git in fact indicates a file is a symlink by setting the tree object's mode to a specific magic number. So there is no git metadata that git-annex can use to track whether a file is supposed to be executable. Therefore, this will only get fixed when there's some kind of full-fledged metadata storage for git. """]]