[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="209.250.56.54"
 subject="comment 4"
 date="2014-10-09T20:43:34Z"
 content="""
Ah, ok. git's index has the file listed as not being a symlink, because `git commit $file` stages it in the index that way. Running `git reset --hard` will fix git's index.

This problem is avoided if you `git annex add $file` before committing. Which is generally a good idea
for other reasons, including avoiding staging a potentially huge file's contents in the git index in the first place.

git-annex's pre-commit hook should probably update the git index for the committed files, replacing the staged full file contents with the git-annex symlink. That would avoid this problem.
"""]]