I looked through some of these answers, fussed with Project Settings, tried a few things, etc. and nothing worked. (Full disclosure: I’m not trying to juggle Gradle here; I’m just using Maven, but I don’t see what this has to do with Gradle.)
I’m using IDEA 14.
What I found to work, because it just simply seemed IntelliJ had lost its way, was this:
$ rm -rf .idea project-name.iml
Then relaunched IntelliJ and did File -> Open -> navigate to the root of my project, etc.–in short, just recreated my project.
IntelliJ got over it. I may have messed something up originally in this project as I had done plenty of refactoring both package- and class names and I had even changed the project name. (It was probably my fault it happened.)