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There is no meta.inf property in project.properties when a new EJB project is created. The entire WS functionality is broken because of this. See the issue 105228.
I can reproduce.
Regression introduced by the fix of issue 97851. Checking in src/org/netbeans/modules/j2ee/ejbjarproject/api/EjbJarProjectGenerator.java; /cvs/j2ee/ejbjarproject/src/org/netbeans/modules/j2ee/ejbjarproject/api/EjbJarProjectGenerator.java,v <-- EjbJarProjectGenerator.java new revision: 1.10; previous revision: 1.9 done