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Issue: The Project tree contains classes twice after finishing the wizard, once in the packages hierarchy, once in the source hierarchy. Analysis: When sources are added via the Sources node and then also marked as Java Roots this duplication appears. This problem is a symptom of the ambiguously communicated relationship of Java and Source roots in the project. Recommendation(s): Java and Source roots as user concepts do not work well. The duplication of files in two places is only one symptom connected with confusion about what a Java root is and what a Source root is when adding files to a project. Removing the user concept may help this problem though more thought needs to go into how to mark sources for inclusion on the classpath (which is really what the Java root represents).
no longer an issue
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 VERIFIED --->
---> CLOSED
Reorganization of java component