The idea of Git eludes you. You don't structure Git projects in a giant directory tree.
The first problem here is that you need to decide, up front, what your structure should be. For pretty much any large project that I've worked on, the correct structure is something that's only apparent 5 years after starting, and 5 years later is different. With git, you have to maintain externals if you want to be able to do a single clone and get the whole repository. Atomic commits (you know, the feature that we moved to svn from cvs for) are then very difficult, because you must commit and push in leaf-to-root order in your git repository nest.