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Compiled Classes target shows one node for every inner class but the name of all of them is the same -- the name of the 'outer' class. This happens when you compile to sources folder. I suggest to leave all nodes but to fix the display name to show OuterClass$InnerClass.
Fixed, but the innerclasses are shown in the outher class, the clazz module is designed in this way.
verified in 200308130000
As described in http://www.netbeans.org/servlets/ReadMsg?msgId=619519&listName=nbdiscuss the current work on projects prototype has been stopped. Marking issue as CLOSED.