At the moment, if you are working with large repositories using multiple makefiles, it is probably still more sensible to just open the top-level directory you are interested in within IntelliJ, then build from a command line.
This still has the advantage of giving you a project-view of the folder. For instance I just opened a folder (instead of a project) nested within ATS-Postiats-contrib:
IntelliJ will still maintain your view state between restarts, but at the cost of creating a '.idea' directory in the top-level directory you have selected. So you may want to add .idea to the repo's .gitignore.
It also has other deficiencies since if you refer to files outside of the hierarchy, you will have to use another method (such as opening a new window to open the ATS-Postiats or ATS-Postiats-contrib repo at top-level). Of course, the plugin does not know how to reference ATSLIB functions (someday I hope).