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In the "Enterprise Beans" subfolder of an EJB Module project, it is not currently possible to right-click and delete individual EJBs. However, if the EJB contains a Web Service annotation, it is possible to right click on that Web Service in the "Web Services" subfolder of the EJB Module and select Delete which deletes the EJB. This is inconsistent behaviour. It should therefore be possible to delete an EJB directly from the Enterprise Beans folder.
This was found in Sierra build Milestone 5 (for Java CAPS 5.2).
Yes, it makes sense, unfortunately not realistic for 6.1
Changing the target to 7.0.
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