I know that you are planning to rework your library support. Have you considered allowing the use of wildcards in the definition of a library, similar to the way in which one defines classpaths in Ant?
I think every project I've worked on has a lib directory, and every jar in lib was supposed to be on the classpath, so I think I would almost always use a wildcard rather than specify individual jars. Also, this makes the project much easier to sync up with other developers who are not using Intellij.
Another thought: you currently have an option for run profiles to compile before running. Have you considered an option to executing an Ant target before running (presumably a "build" target)?
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