Program: 120657
Project: 120657
Buggy source:
protected void processRename(RepositoryNode node,String originalName){
  try {
    IJavaProject javaProject=CorePlugin.getDefault().getRunProcessService().getJavaProject();
    if (javaProject == null) {
      return;
    }
    IProject project=javaProject.getProject();
    IFolder srcFolder=project.getFolder(JavaUtils.JAVA_SRC_DIRECTORY);
    IPackageFragmentRoot root=javaProject.getPackageFragmentRoot(srcFolder);
    IPackageFragment routinesPkg=getPackageFragment(root);
    ICompilationUnit unit=routinesPkg.getCompilationUnit(originalName + SuffixConstants.SUFFIX_STRING_java);
    if (unit == null) {
      return;
    }
    String newName=node.getObject().getProperty().getLabel();
    JavaRenameProcessor processor=new RenameCompilationUnitProcessor(unit);
    processor.setNewElementName(newName + SuffixConstants.SUFFIX_STRING_java);
    RenameRefactoring ref=new RenameRefactoring(processor);
    final PerformRefactoringOperation operation=new PerformRefactoringOperation(ref,CheckConditionsOperation.ALL_CONDITIONS);
    IRunnableWithProgress r=new IRunnableWithProgress(){
      @Override public void run(      final IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
        Display.getDefault().asyncExec(new Runnable(){
          @Override public void run(){
            try {
              operation.run(monitor);
            }
 catch (            CoreException e) {
              ExceptionHandler.process(e);
            }
          }
        }
);
      }
    }
;
    PlatformUI.getWorkbench().getProgressService().run(true,true,r);
    RefactoringStatus conditionStatus=operation.getConditionStatus();
    if (conditionStatus.hasError()) {
      String errorMessage=Messages.getString("String_Node_Str",unit.getElementName(),newName);
      RefactoringStatusEntry[] entries=conditionStatus.getEntries();
      for (      RefactoringStatusEntry entry : entries) {
        errorMessage+="String_Node_Str" + entry.getMessage();
      }
      Shell shell=null;
      IRepositoryView viewPart=getViewPart();
      if (viewPart != null) {
        shell=viewPart.getViewSite().getShell();
      }
 else {
        shell=Display.getCurrent().getActiveShell();
      }
      MessageDialog.openError(shell,Messages.getString("String_Node_Str"),errorMessage);
      return;
    }
    ICompilationUnit newUnit=routinesPkg.getCompilationUnit(newName + SuffixConstants.SUFFIX_STRING_java);
    if (newUnit == null) {
      return;
    }
    RoutineItem item=(RoutineItem)node.getObject().getProperty().getItem();
    IFile javaFile=(IFile)newUnit.getAdapter(IResource.class);
    try {
      ByteArray byteArray=item.getContent();
      byteArray.setInnerContentFromFile(javaFile);
      IRepositoryService service=CorePlugin.getDefault().getRepositoryService();
      IProxyRepositoryFactory repFactory=service.getProxyRepositoryFactory();
      repFactory.save(item);
    }
 catch (    Exception e) {
      ExceptionHandler.process(e);
    }
  }
 catch (  Exception e) {
    ExceptionHandler.process(e);
  }
}

Fixed version (ground truth):
protected void processRename(RepositoryNode node,String originalName){
  try {
    IJavaProject javaProject=CorePlugin.getDefault().getRunProcessService().getJavaProject();
    if (javaProject == null) {
      return;
    }
    IProject project=javaProject.getProject();
    IFolder srcFolder=project.getFolder(JavaUtils.JAVA_SRC_DIRECTORY);
    IPackageFragmentRoot root=javaProject.getPackageFragmentRoot(srcFolder);
    IFolder srcInterFolder=srcFolder.getFolder("String_Node_Str");
    if (srcInterFolder.exists()) {
      File file=new File(srcInterFolder.getLocationURI());
      for (      File f : file.listFiles()) {
        if (f.isFile()) {
          f.delete();
        }
      }
    }
    IPackageFragment routinesPkg=getPackageFragment(root);
    ICompilationUnit unit=routinesPkg.getCompilationUnit(originalName + SuffixConstants.SUFFIX_STRING_java);
    if (unit == null) {
      return;
    }
    String newName=node.getObject().getProperty().getLabel();
    JavaRenameProcessor processor=new RenameCompilationUnitProcessor(unit);
    processor.setNewElementName(newName + SuffixConstants.SUFFIX_STRING_java);
    RenameRefactoring ref=new RenameRefactoring(processor);
    final PerformRefactoringOperation operation=new PerformRefactoringOperation(ref,CheckConditionsOperation.ALL_CONDITIONS);
    IRunnableWithProgress r=new IRunnableWithProgress(){
      @Override public void run(      final IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
        Display.getDefault().asyncExec(new Runnable(){
          @Override public void run(){
            try {
              operation.run(monitor);
            }
 catch (            CoreException e) {
              ExceptionHandler.process(e);
            }
          }
        }
);
      }
    }
;
    PlatformUI.getWorkbench().getProgressService().run(true,true,r);
    RefactoringStatus conditionStatus=operation.getConditionStatus();
    if (conditionStatus.hasError()) {
      String errorMessage=Messages.getString("String_Node_Str",unit.getElementName(),newName);
      RefactoringStatusEntry[] entries=conditionStatus.getEntries();
      for (      RefactoringStatusEntry entry : entries) {
        errorMessage+="String_Node_Str" + entry.getMessage();
      }
      Shell shell=null;
      IRepositoryView viewPart=getViewPart();
      if (viewPart != null) {
        shell=viewPart.getViewSite().getShell();
      }
 else {
        shell=Display.getCurrent().getActiveShell();
      }
      MessageDialog.openError(shell,Messages.getString("String_Node_Str"),errorMessage);
      return;
    }
    ICompilationUnit newUnit=routinesPkg.getCompilationUnit(newName + SuffixConstants.SUFFIX_STRING_java);
    if (newUnit == null) {
      return;
    }
    RoutineItem item=(RoutineItem)node.getObject().getProperty().getItem();
    IFile javaFile=(IFile)newUnit.getAdapter(IResource.class);
    try {
      ByteArray byteArray=item.getContent();
      byteArray.setInnerContentFromFile(javaFile);
      IRepositoryService service=CorePlugin.getDefault().getRepositoryService();
      IProxyRepositoryFactory repFactory=service.getProxyRepositoryFactory();
      repFactory.save(item);
    }
 catch (    Exception e) {
      ExceptionHandler.process(e);
    }
  }
 catch (  Exception e) {
    ExceptionHandler.process(e);
  }
}