Program: 137864
Project: 137864
Buggy source:
@Override public void run(){
  ISelection selection=this.getSelection();
  Object[] deleteElements=((IStructuredSelection)selection).toArray();
  if (deleteElements.length == 0) {
    return;
  }
  if (forbiddenDeleteJrxmlFileFolder(deleteElements)) {
    return;
  }
  deleteElements=checkSourceFilesEditorOpening(deleteElements);
  for (  Object obj : deleteElements) {
    if (obj instanceof RepositoryNode) {
      selectedNodes.add((RepositoryNode)obj);
    }
  }
  if (DQRepositoryNode.isOnFilterring()) {
    if (deleteElements[0] instanceof RepositoryNode) {
      setPreviousFilteredNode((RepositoryNode)deleteElements[0]);
    }
    for (    RepositoryNode node : selectedNodes) {
      RepositoryNodeHelper.removeChildrenNodesWhenFiltering(node);
    }
  }
  List deleteNodes=null;
  List<IRepositoryNode> shownNodes=null;
  List<IRepositoryNode> findAllRecycleBinNodes=null;
  if (DQRepositoryNode.isOnFilterring()) {
    deleteNodes=new ArrayList();
    Collections.addAll(deleteNodes,deleteElements);
    shownNodes=RepositoryNodeHelper.findAllChildrenNodes(deleteNodes);
    List<IRepositoryNode> recycleBinNodeFirstLevelChildren=((RepositoryNode)RepositoryNodeHelper.getRecycleBinRepNode()).getChildren();
    findAllRecycleBinNodes=RepositoryNodeHelper.findAllChildrenNodes(recycleBinNodeFirstLevelChildren);
  }
  for (int i=selectedNodes.size() - 1; i >= 0; i--) {
    if (selectedNodes.size() == 0) {
      break;
    }
    RepositoryNode node=selectedNodes.get(i);
    RepositoryNode parent=node.getParent();
    if (node instanceof ReportFileRepNode) {
      deleteReportFile((ReportFileRepNode)node);
      continue;
    }
    boolean isStateDeleted=RepositoryNodeHelper.isStateDeleted(node);
    if (!isStateDeleted) {
      excuteSuperRun(null,parent);
      break;
    }
    if (DQRepositoryNode.isOnFilterring() && isStateDeleted) {
      for (      IRepositoryNode iRepositoryNode : findAllRecycleBinNodes) {
        if (node.equals(iRepositoryNode)) {
          node=(RepositoryNode)iRepositoryNode;
          shownNodes=RepositoryNodeHelper.findAllChildrenNodes(deleteNodes);
          break;
        }
      }
      if (!RepositoryNodeHelper.isEmptyRecycleBin(findAllRecycleBinNodes,shownNodes)) {
        break;
      }
    }
    boolean hasDependency=false;
    if (node.getType() == ENodeType.SIMPLE_FOLDER || node.getType() == ENodeType.SYSTEM_FOLDER) {
      List<IRepositoryNode> newLs=RepositoryNodeHelper.getRepositoryElementFromFolder(node,true);
      boolean haveSubNode=false;
      for (      IRepositoryNode subNode : newLs) {
        hasDependency=RepositoryNodeHelper.hasDependencyClients(subNode);
        if (!hasDependency || hasDependency && handleDependencies(subNode)) {
          excuteSuperRun((RepositoryNode)subNode,node);
        }
 else {
          haveSubNode=true;
        }
      }
      if (!haveSubNode) {
        excuteSuperRun(node,parent);
      }
    }
 else {
      hasDependency=RepositoryNodeHelper.hasDependencyClients(node);
      if (!hasDependency || hasDependency && handleDependencies(node)) {
        excuteSuperRun(node,parent);
      }
    }
  }
  if (DQRepositoryNode.isOnFilterring()) {
    RepositoryNodeHelper.regainRecycleBinFilteredNode();
  }
  CorePlugin.getDefault().refreshWorkSpace();
  CorePlugin.getDefault().refreshDQView(RepositoryNodeHelper.getRecycleBinRepNode());
}

Fixed version (ground truth):
public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
  IWorkspace workspace=ResourcesPlugin.getWorkspace();
  try {
    ISchedulingRule schedulingRule=workspace.getRoot();
    workspace.run(op,schedulingRule,IWorkspace.AVOID_UPDATE,monitor);
  }
 catch (  CoreException e) {
    throw new InvocationTargetException(e);
  }
}