[Git submodules](http://git-scm.com/book/en/v2/Git-Tools-Submodules) are
supported by git-annex since version 5.20150303.

Git normally makes a `.git` **file** in a
submodule, that points to the real git repository under `.git/modules/`.
This presents problems for git-annex. So, when used in a submodule,
git-annex will automatically replace the `.git` file with a symlink
pointing at the git repository. (When the filesystem doesn't support
symlinks, an adjusted unlocked branch is used, and submodules are
supported in that setup too.)

With that taken care of, git-annex should work ok in submodules. Although
this is a new and somewhat experimental feature.

The conversion of .git file to .git symlink mostly won't bother git.

Known problems:

* If you want to delete a whole submodule, `git rm submodule`
  will refuse to delete it, complaining that the
  submodule "uses a .git directory". Workaround: Use `rm -rf`
  to delete the tree, and then `git commit`.