Program: 118822
Project: 118822
Buggy source:
@Override public ExecutionResult execute(Item item){
  if (item.getProperty().getAuthor() == null) {
    IProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
    item.getProperty().setAuthor(factory.getRepositoryContext().getUser());
  }
  if (ERepositoryObjectType.getItemType(item).isDQItemType() && !ERepositoryObjectType.getItemType(item).isDIItemType()) {
    return ExecutionResult.NOTHING_TO_DO;
  }
  if (item.getProperty().getAuthor().getLogin() != null) {
    return ExecutionResult.NOTHING_TO_DO;
  }
  IProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
  item.getProperty().setAuthor(factory.getRepositoryContext().getUser());
  XmiResourceManager manager=ProxyRepositoryFactory.getInstance().getRepositoryFactoryFromProvider().getResourceManager();
  List<Resource> toDelete=new ArrayList<Resource>();
  for (  Resource resource : manager.resourceSet.getResources()) {
    if (resource.getURI().toString().contains(manager.getProjectFilename())) {
      try {
        IFile file=URIHelper.getFile(resource.getURI());
        if (!file.exists()) {
          toDelete.add(resource);
        }
      }
 catch (      Exception e) {
        toDelete.add(resource);
      }
    }
  }
  EmfHelper.visitChilds(item);
  try {
    factory.save(item,true);
  }
 catch (  PersistenceException e) {
    ExceptionHandler.process(e);
  }
catch (  UnsupportedOperationException e1) {
    ExceptionHandler.process(e1);
  }
  manager.resourceSet.getResources().removeAll(toDelete);
  return ExecutionResult.SUCCESS_NO_ALERT;
}

Fixed version (ground truth):
@Override public ExecutionResult execute(Item item){
  if (item.getProperty().getAuthor() == null) {
    IProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
    item.getProperty().setAuthor(factory.getRepositoryContext().getUser());
  }
  if (ERepositoryObjectType.getItemType(item).isDQItemType() && !ERepositoryObjectType.getItemType(item).isDIItemType()) {
    return ExecutionResult.NOTHING_TO_DO;
  }
  if (item.getProperty().getAuthor().getLogin() != null) {
    return ExecutionResult.NOTHING_TO_DO;
  }
  IProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
  item.getProperty().setAuthor(factory.getRepositoryContext().getUser());
  clearReferenceResourcesFileName(item);
  XmiResourceManager manager=ProxyRepositoryFactory.getInstance().getRepositoryFactoryFromProvider().getResourceManager();
  List<Resource> toDelete=new ArrayList<Resource>();
  for (  Resource resource : manager.resourceSet.getResources()) {
    if (resource.getURI().toString().contains(manager.getProjectFilename())) {
      try {
        IFile file=URIHelper.getFile(resource.getURI());
        if (!file.exists()) {
          toDelete.add(resource);
        }
      }
 catch (      Exception e) {
        toDelete.add(resource);
      }
    }
  }
  EmfHelper.visitChilds(item);
  try {
    factory.save(item,true);
  }
 catch (  PersistenceException e) {
    ExceptionHandler.process(e);
  }
catch (  UnsupportedOperationException e1) {
    ExceptionHandler.process(e1);
  }
  manager.resourceSet.getResources().removeAll(toDelete);
  return ExecutionResult.SUCCESS_NO_ALERT;
}