Source, Resources, or Test Directories for WordPress Theme Development?

I just started using PHPStorm to develop my themes. When I first started using the IDE, I'd only added my acual theme directory as a project. When I would go to reference a WP function in my theme, PHPStorm couldn't find the core function because it wasn't in my project. For instance, in my theme, I'd cmd-click on the get_footer(); function and PHPStorm could find it.

To remedy that, I add all of my WordPress installation to the project. Now when I open the project I have to drill down to my theme's directory each time, Grunt doesn't work out like it did when only the theme was the project.

How do I keep the WP core files in the project for references and mark the theme's directory as the main part of my project for Terminal and Grunt references?