Is there a preferred way to add files to git's index (instead of the annex) while in direct mode?

I am trying to use git-annex for scientific data. On linux and mac in indirect mode, the git workflow is basically unchanged, and I really like the way git annex works. Unfortunately when I use git-annex on Windows, I have not found a good way to add things to git's tree.

I've tried two things:

$ git annex proxy -- git add smallfile

This is slow because it has to copy things over to create a work tree

$ git config annex.largefiles="*.pdf or *.h5"
$ git annex add largefile.pdf

This doesn't seem to work as well as I'd like either. I'd like the equivalent of a git add command in direct mode.