Mark Directory As... seems impermanent

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I seem to be having this problem, but in IntelliJ IDEA. I have a Scala project (Maven) and I mark the src/main/scala directory as Sources Root. But after a series of events I haven't really nailed down, it starts complaining that it can't find classes with 'main.scala.' prepended to the package, and the src directory is marked as Sources Root. Is that clear? My sources root seems to keep moving down to src in the project folder.

Why is this? How do I stop it?

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