[[!comment format=mdwn
 username="http://joeyh.name/"
 nickname="joey"
 subject="comment 5"
 date="2013-04-16T21:25:45Z"
 content="""
In a direct mode repository, until you commit changes to a file, `git annex whereis` and most other git-annex commands will operate on the version that was last committed to git.

That seems to be the source of your confusion.

I think this can be confusing.. It might make sense for git-annex whereis to skip over modified files in direct mode.
"""]]