Git Submodules Are Not That Bad
Fleetinggit submodules are often used when one wants to have several repositories in sync. Then, one just gets pissed of the choreography needed to sync them (commit on the submodule, then commit on the parent).
I think this is a symptom of not correctly asking the question. git submodule do the job in a very great way, particularly when you are keen on reproducible research. But one generally uses submodule when one does not know exactly what they want to achieve but they realize they have to deal with several teams working on several part of some product.