Michael, this one is for you .. :)
We have the following structure in ClearCase - 1.png, 2.png.
The "workspace" folder contains the super-POM file aggregating POMs from 3 other modules - "poc", "pocfe", and "pocUtils" (exactly as in http://maven.apache.org/guides/introduction/introduction-to-the-pom.html , Example 4).
IDEA project was generated from opening the "workspace/pom.xml". Now what I see in IDEA is 3.png, i.e pom.xml from the "workspace" folder that gave birth to the whole project didn't became part of, say, "workspace" module, it belongs to no module at all.
As a result - I can't check out "workspace/pom.xml" from IDEA: right click -> ClearCase -> Check Out has no effect. Also, if I check out "workspace/pom.xml" externally using CC Explorer - IDEA doesn't see it, it doesn't modify it's color in file tabs after synchronizing the project status (CtrlAltY)