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+[[!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.
+"""]]