Gradle Multi Modules with Multiple Source Sets

So, as many are aware, 16 adds multi-source sets as separated modules. While I welcome this for finer granularity control of which dependencies are managed in which source set, the current setup completely breaks usability of IntelliJ with my project that I work on a daily basis.

The project itself has two git submodules and likewise those two projects are gradle submodules. The project is accessible here, and

an image of what the project looks like in IntelliJ 15:

And while it works fine and compiles, there's a few things set up, such as a Java 6 specific launcher source set that is set to be compiled in Java 6, while the rest of the project is compiled in Java 8.

What the project looks like in IntelliJ 16:

And what happens here is that the modules lose their dependencies that normally compile just fine, even gradle compiles just fine to the point that re-arranging and re-adding all the dependencies for each specific source set is required. 

My biggest issue with all of this is: Jetbrains doesn't seem to have replied or acknowledged that the related issue is going to be fixed or being worked on. So, I'm asking here, is there something that I can do for the project to re-arrange the gradle submodules to properly support all the dependencies?