[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="4.154.0.63"
 subject="comment 1"
 date="2013-08-24T18:49:18Z"
 content="""
git-annex assumes that it can make a stable symlink from a file in the working tree to a file in the .git directory. There are several ways to break this. One, as noted, is sometimes using a repository as a submodule, and sometimes not. Another would be to play around with `GIT_DIR`.

I don't see a way git-annex can support those use cases, at least in indirect mode.

It does seem like, in direct mode, it should just work. git-annex will commit various symlinks to git, but these symlinks will never be followed to get at the content of a file, since direct mode arranges for the content to be directly present in the working tree.
"""]]