[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2015-02-04T17:19:46Z"
 content="""
git-annex should have no difficulty doing that, and in fact its test
suite includes some adds of files in subdirs.

The most likely reason for this behavior would be if you have configured
a `.gitignore` file (or other method of configuring gitignore) to 
exclude the file you want to add. If so, "git annex add --force
mydir/myfile" would override the gitignore.

Internally, git-annex add runs "git ls-files --others --exclude-standard"
and passes it the files/dirs you specified to add, and then adds
the files that command lists. So you can run that command and see
what it lists too.
"""]]
