title: Eclipse refactoring fails -> Keeps throwing exceptions!
body: <p>I'm using Eclipse Helios and for every refactoring that spans multiple files it plainly fails! Nothing happens. On examining the logs here's the error that I see:</p>
  
  <pre><code>!ENTRY org.eclipse.ltk.ui.refactoring 4 10000 2011-03-13 14:15:31.842
  !MESSAGE Internal Error
  !STACK 0
  
  java.lang.reflect.InvocationTargetException
  at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:421)
  at org.eclipse.ltk.internal.ui.refactoring.RefactoringWizardDialog2.run(RefactoringWizardDialog2.java:330)
  at org.eclipse.ltk.ui.refactoring.RefactoringWizard.internalPerformFinish(RefactoringWizard.java:573)
  at org.eclipse.ltk.ui.refactoring.UserInputWizardPage.performFinish(UserInputWizardPage.java:153)
  at org.eclipse.jdt.internal.ui.refactoring.reorg.RenameTypeWizardInputPage.performFinish(RenameTypeWizardInputPage.java:144)
  at org.eclipse.ltk.ui.refactoring.RefactoringWizard.performFinish(RefactoringWizard.java:646)
  at org.eclipse.ltk.internal.ui.refactoring.RefactoringWizardDialog2.okPressed(RefactoringWizardDialog2.java:454)
  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:234)
  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:4066)
  at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
  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:180)
  at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
  at org.eclipse.ltk.ui.refactoring.RefactoringWizardOpenOperation.run(RefactoringWizardOpenOperation.java:192)
  at org.eclipse.ltk.ui.refactoring.RefactoringWizardOpenOperation.run(RefactoringWizardOpenOperation.java:115)
  at org.eclipse.jdt.internal.ui.refactoring.actions.RefactoringStarter.activate(RefactoringStarter.java:38)
  at org.eclipse.jdt.internal.ui.refactoring.UserInterfaceStarter.activate(UserInterfaceStarter.java:62)
  at org.eclipse.jdt.internal.ui.refactoring.reorg.RenameUserInterfaceStarter.activate(RenameUserInterfaceStarter.java:31)
  at org.eclipse.jdt.ui.refactoring.RenameSupport.openDialog(RenameSupport.java:159)
  at org.eclipse.jdt.ui.refactoring.RenameSupport.openDialog(RenameSupport.java:116)
  at org.eclipse.jdt.internal.corext.refactoring.RefactoringExecutionStarter.startRenameRefactoring(RefactoringExecutionStarter.java:438)
  at org.eclipse.jdt.internal.ui.refactoring.actions.RenameJavaElementAction.run(RenameJavaElementAction.java:203)
  at org.eclipse.jdt.internal.ui.refactoring.actions.RenameJavaElementAction.run(RenameJavaElementAction.java:101)
  at org.eclipse.jdt.ui.actions.RenameAction.run(RenameAction.java:108)
  at org.eclipse.jdt.ui.actions.SelectionDispatchAction.dispatchRun(SelectionDispatchAction.java:274)
  at org.eclipse.jdt.ui.actions.SelectionDispatchAction.run(SelectionDispatchAction.java:250)
  at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
  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:4066)
  at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
  at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2640)
  at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2604)
  at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
  at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
  at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
  at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
  at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
  at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
  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:369)
  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:619)
  at org.eclipse.equinox.launcher.Main.basicRun(Main.java:574)
  at org.eclipse.equinox.launcher.Main.run(Main.java:1407)
  Caused by: java.lang.NoClassDefFoundError: org/eclipse/jst/jsp/core/internal/java/search/JSPIndexManager
  at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.searchRunnable(JSPSearchSupport.java:424)
  at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.searchRunnable(JSPSearchSupport.java:349)
  at org.eclipse.jst.jsp.ui.internal.java.refactoring.JSPRenameParticipant.createChangesFor(JSPRenameParticipant.java:215)
  at org.eclipse.jst.jsp.ui.internal.java.refactoring.JSPRenameParticipant.createChange(JSPRenameParticipant.java:153)
  at org.eclipse.ltk.core.refactoring.participants.ProcessorBasedRefactoring.createChange(ProcessorBasedRefactoring.java:308)
  at org.eclipse.ltk.core.refactoring.CreateChangeOperation.run(CreateChangeOperation.java:124)
  at org.eclipse.ltk.core.refactoring.PerformChangeOperation.run(PerformChangeOperation.java:209)
  at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
  at org.eclipse.ltk.internal.ui.refactoring.WorkbenchRunnableAdapter.run(WorkbenchRunnableAdapter.java:87)
  at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:121)
  Root exception:
  java.lang.NoClassDefFoundError: org/eclipse/jst/jsp/core/internal/java/search/JSPIndexManager
  at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.searchRunnable(JSPSearchSupport.java:424)
  at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.searchRunnable(JSPSearchSupport.java:349)
  at org.eclipse.jst.jsp.ui.internal.java.refactoring.JSPRenameParticipant.createChangesFor(JSPRenameParticipant.java:215)
  at org.eclipse.jst.jsp.ui.internal.java.refactoring.JSPRenameParticipant.createChange(JSPRenameParticipant.java:153)
  at org.eclipse.ltk.core.refactoring.participants.ProcessorBasedRefactoring.createChange(ProcessorBasedRefactoring.java:308)
  at org.eclipse.ltk.core.refactoring.CreateChangeOperation.run(CreateChangeOperation.java:124)
  at org.eclipse.ltk.core.refactoring.PerformChangeOperation.run(PerformChangeOperation.java:209)
  at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
  at org.eclipse.ltk.internal.ui.refactoring.WorkbenchRunnableAdapter.run(WorkbenchRunnableAdapter.java:87)
  at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:121)
  </code></pre>
  
  <p>This error doesn't make much sense for me to be able to navigate around and even 'try' fixing it. For refactorings that are 'local' to the file/methods it seems to work fine. I've tried figuring this one out but just aghast! I tend to use the refactor feature A LOT. I'm working with J2EE + Glassfish v3. I have JARs for freemarker, restlet and that for DBUtils on the build path.</p>
  
  <p>Any ideas? Has anyone encountered (and fixed :) this problem??</p>
  
  <p>Thanks in advance!</p>