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Most J2EE projects contain more than simply WAR and EJB components. It would be nice if NetBeans could fully support the J2EE project convention as defined by the Sun Java BluePrints (http://java.sun.com/blueprints/code/projectconventions.html see figure 1.1 and table 1.1) rather than a subset of it.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss