Skimming through the SubModule tutorial, I created a submodule out of the boto project. Then, I discovered that I actually need only a subset of this project - specifically,
What you want to do is create a branch in the submodule and move the folder up and delete what you don't need. You can then manage that branch instead. If you want to push up your changes, you should be able to back merge first. Git will know that you moved the files and do the merge successfully.
Hope this helps.