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Under web application node there are server's applications visible and it's possible to perform undeploy on them. They shouldn't be visible.
I would not hide the applications, we might only disable the undeploy action for those applications.
*** Issue 105548 has been marked as a duplicate of this issue. ***
Fixed jbossws-context, however root application remains visible because it is not system application and deploying to root context is common use case. The problem of the deployment to the existing context should be solved by fixing issue 91792. Checking in src/org/netbeans/modules/j2ee/jboss4/JBDeployer.java; /cvs/serverplugins/jboss4/src/org/netbeans/modules/j2ee/jboss4/JBDeployer.java,v <-- JBDeployer.java new revision: 1.16; previous revision: 1.15 done Checking in src/org/netbeans/modules/j2ee/jboss4/nodes/JBEarModulesChildren.java; /cvs/serverplugins/jboss4/src/org/netbeans/modules/j2ee/jboss4/nodes/JBEarModulesChildren.java,v <-- JBEarModulesChildren.java new revision: 1.5; previous revision: 1.4 done Checking in src/org/netbeans/modules/j2ee/jboss4/nodes/JBWebApplicationsChildren.java; /cvs/serverplugins/jboss4/src/org/netbeans/modules/j2ee/jboss4/nodes/JBWebApplicationsChildren.java,v <-- JBWebApplicationsChildren.java new revision: 1.5; previous revision: 1.4 done Checking in src/org/netbeans/modules/j2ee/jboss4/nodes/Util.java; /cvs/serverplugins/jboss4/src/org/netbeans/modules/j2ee/jboss4/nodes/Util.java,v <-- Util.java new revision: 1.7; previous revision: 1.6 done