Look, this will make the git history look funny, but trimming unnecessary depth from the source tree is a very necessary sanity-preserving measure when dealing with a super-modularized codebase like this one.
While it makes the project configuration a bit less conventional, it will save you several clicks every time you jump between modules. Which you'll do a lot, because it's *modul*ar. The src/main/java convention makes a lot of sense for a non-modular project though. This ain't that.
