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Create a JPA project as follows - - File > New > JPA Project - Enter name (JPA 2.0 EL 2.0 Project) - Check Add project to an Ear checkbox - Click on New Project button - Enter Ear Project for name and check Add project to working sets checkbox - Click on Select button, Click on New button on Select Working Sets dialog - Enter Working Set for the name and click on Finish - Check the Working Set checkbox and click OK - Click on the Next button and then on the New Module button - Uncheck EJB Client checkbox and Conector module checkbox and click on Finish - Click on Finish button for New EAR Application Project dialog - Check the Add Project to Working Sets checkbox and click on Select button - Check the Working Set checkbox and click on OK button - Finish the project creation and 4 items appear in the Project Explorer (Ear Project, Ear ProjectClient, Ear ProjectWeb, JPA 2.0 EL 2.0 Project) Delete the JPA 2.0 EL 2.0 Project and all it contents Delete the Ear ProjectWeb and all it contents Delete the Ear ProjectClient and all its contents Finally Delete the Ear Project and all its contents When you delete the last item (Ear Project) 4 NPE errors appear in the error log java.lang.NullPointerException at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.detectURIMapping(ProjectResourceSetImpl.java:761) at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.createResource(ProjectResourceSetImpl.java:779) at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.createModelResource(JEE5ModelProvider.java:192) at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.getModelResource(JEE5ModelProvider.java:174) at org.eclipse.jst.jee.model.internal.EAR5ModelProvider.getModelObject(EAR5ModelProvider.java:53) at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.getModelObject(JEE5ModelProvider.java:217) at org.eclipse.jst.jee.ui.internal.navigator.Ear5ContentProvider.getNewContentProviderInstance(Ear5ContentProvider.java:152) at org.eclipse.jst.jee.ui.internal.navigator.JEE5ContentProvider.getCachedContentProvider(JEE5ContentProvider.java:92) at org.eclipse.jst.jee.ui.internal.navigator.Ear5ContentProvider.getChildren(Ear5ContentProvider.java:116) at org.eclipse.ui.internal.navigator.extensions.SafeDelegateTreeContentProvider.getChildren(SafeDelegateTreeContentProvider.java:96) at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider$1.run(NavigatorContentServiceContentProvider.java:152) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.internalGetChildren(NavigatorContentServiceContentProvider.java:139) at org.eclipse.ui.internal.navigator.NavigatorContentServiceContentProvider.getChildren(NavigatorContentServiceContentProvider.java:119) at org.eclipse.jst.jee.ui.internal.navigator.JEE5ContentProvider$1.run(JEE5ContentProvider.java:127) at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35) at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135) at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4140) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3757) at org.eclipse.jface.operation.ModalContext$ModalContextThread.block(ModalContext.java:173) at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:388) at org.eclipse.ltk.internal.ui.refactoring.RefactoringWizardDialog2.run(RefactoringWizardDialog2.java:331) at org.eclipse.ltk.ui.refactoring.RefactoringWizard.internalPerformFinish(RefactoringWizard.java:605) at org.eclipse.ltk.ui.refactoring.UserInputWizardPage.performFinish(UserInputWizardPage.java:153) at org.eclipse.ltk.ui.refactoring.resource.DeleteResourcesWizard$DeleteResourcesRefactoringConfigurationPage.performFinish(DeleteResourcesWizard.java:151) at org.eclipse.ltk.ui.refactoring.RefactoringWizard.performFinish(RefactoringWizard.java:678) at org.eclipse.ltk.internal.ui.refactoring.RefactoringWizardDialog2.okPressed(RefactoringWizardDialog2.java:455) at org.eclipse.jface.dialogs.Dialog.buttonPressed(Dialog.java:472) at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:624) at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:240) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053) at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4165) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3754) at org.eclipse.jface.window.Window.runEventLoop(Window.java:825) at org.eclipse.jface.window.Window.open(Window.java:801) at org.eclipse.ltk.ui.refactoring.RefactoringWizardOpenOperation$1.run(RefactoringWizardOpenOperation.java:181) at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70) at org.eclipse.ltk.ui.refactoring.RefactoringWizardOpenOperation.run(RefactoringWizardOpenOperation.java:193) at org.eclipse.ltk.ui.refactoring.RefactoringWizardOpenOperation.run(RefactoringWizardOpenOperation.java:116) at org.eclipse.ltk.internal.ui.refactoring.actions.DeleteResourcesHandler.execute(DeleteResourcesHandler.java:40) at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293) at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476) at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508) at org.eclipse.ui.internal.handlers.HandlerService.executeCommandInContext(HandlerService.java:270) at org.eclipse.ui.internal.ide.actions.LTKLauncher.runCommand(LTKLauncher.java:95) at org.eclipse.ui.internal.ide.actions.LTKLauncher.openDeleteWizard(LTKLauncher.java:47) at org.eclipse.ui.actions.DeleteResourceAction.run(DeleteResourceAction.java:474) at org.eclipse.ui.actions.BaseSelectionListenerAction.runWithEvent(BaseSelectionListenerAction.java:168) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053) at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4165) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3754) at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696) at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660) at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494) at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332) at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667) at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149) at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577) at org.eclipse.equinox.launcher.Main.run(Main.java:1410) at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
I believe this is a Java EE Tools bug.
This happened in I-3.4.0-20110822071621.
