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If you call Stop on application node, the node changes badge icon and all actions on it are disabled except Undeploy. If you click on it, it opens dialog "Action cannot be performed at this moment. Try few minutes later." It should be also disabled.
This may or may not help -I cannot test it. 44a859d022f2
Integrated into 'main-golden', will be available in build *201204200400* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main-golden/rev/44a859d022f2 User: David Konecny <dkonecny@netbeans.org> Log: #203488 - Undeploy should be disabled when changing state