[[!comment format=mdwn
 username="http://joeyh.name/"
 nickname="joey"
 subject="comment 1"
 date="2013-06-15T18:50:45Z"
 content="""
Joe, you need to carefully read [[direct_mode]]. When you manually run `git merge` in a direct mode repository, you defeat associated file tracking, with the resulting behavior you describe. This is why there is a [[todo/direct_mode_guard]] todo item.
"""]]