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As far as I can see there is no way to create or edit the application.xml in an EAR project in the IDE's GUI. (See also [1].) It would be really handy if there was a GUI for it, for example to allow the user to easily set the context root. [1] http://stackoverflow.com/questions/4758787/how-do-i-change-the-context-path-of-my-enterprise-project
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