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singleton instance in org/netbeans/modules/xml/text/navigator/NavigatorContent.java keeps reference to last shown panel. This can be for instance o.n.m.bpel.navigator.BpelNavigatorPanelholding all the data associated with the BPEL process even when the project is closed.
Fix integrated, see http://hg.netbeans.org/main?cmd=changeset;node=69f102e5cf5a.