[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2016-04-20T18:09:37Z"
 content="""
Seems that there are two potential bugs here; a file that was stored in git
somehow got stored in the annex instead, and something seems to have
happened to the content of the file in the annex.

Try using `git annex log` to see where the content of the file was
stored in the past and when the content got marked as no longer being
present.

A looser annex.largefiles setting could result in a modified file
that had been stored in git being stored in the annex instead.
Look at the symlink that was checked into git for the annexed file
and compare that with the sha256sum of the file that you rescued
from the git history. Are they the same or different?
"""]]