Git submodules are pretty cool, except for kind of sucking. Things I don't recommend doing if you value your sanity:

• Switching a submodule from one repository to another (i.e., editing .gitmodules and changing the repo url)
• Switching a directory from a submodule to regular content
• Switching a directory with regular content to a submodule (though this might help you)

It's a shame, because submodules are pretty handy. But you'll probably end up wanting to do one of these things during the lifetime of your project, and then you're screwed.