In IDEA 3.0, if you had the following source structure:
you could select the folder containing package2 as a project path. IDEA would then "automagically" pick up that src was the sourcepath for your project.
In IDEA 4.0, if I select package2 as a Content Root of a module, then I can only mark the Content Root or one of its child folders as source folders.
So, from what I can understand, I don't think the previous use case can be done as simply as before. The only way to do it would be to select src as the Content Root, and then exclude everything apart from the package you're interested in.
Is my understanding correct here? If so, this situation seems rather more ackward in IDEA 4.0 than in IDEA 3.0.