Thank you very much for the fast reply! This is a much cleaner approach and everything appears to be working perfectly.
Just to be sure though, when pushing to Git I will need to include both projects, as well as the original MASON folder that I linked as "existing source" in the master project. Is that correct? Also, how would I go about building a deployable file once my simulation
I use NetBeans, and I keep things clean by keeping MASON in one project, and writing all of my custom code in its own, separate project.
In the project where you'll write your own model, right-click on "Libraries," select "Add Project," and choose the project you created for MASON. This hooks your project up with a MASON jar but won't clutter your source directory.