Program: 138799
Project: 138799
Buggy source:
@Override protected boolean doExecute() throws Exception {
  EMFUtil emfUtil=new EMFUtil();
  for (  File file : fileList) {
    if (file.isFile()) {
      URI uri=URI.createFileURI(file.getAbsolutePath());
      System.out.println("String_Node_Str" + uri.toString());
      Resource resource=emfUtil.getResourceSet().getResource(uri,true);
      EObject eObject=resource.getContents().get(0);
      if (FactoriesUtil.isProvFile(uri.fileExtension())) {
        for (        EObject object : resource.getContents()) {
          if (object instanceof Connection) {
            eObject=object;
            break;
          }
        }
      }
      if (eObject != null) {
        if (eObject instanceof ModelElement) {
          ModelElement modelElement=(ModelElement)eObject;
          AElementPersistance writer=ElementWriterFactory.getInstance().create(uri.fileExtension());
          Property oldPropery=PropertyHelper.getProperty(modelElement);
          if (writer != null) {
            Property property=writer.initProperty(modelElement);
            if (oldPropery != null) {
              property.setAuthor(oldPropery.getAuthor());
              property.getItem().setState(oldPropery.getItem().getState());
            }
            computePath(property,file);
            URI propURI=resource.getURI().trimFileExtension().appendFileExtension(FactoriesUtil.PROPERTIES_EXTENSION);
            Resource propResource=emfUtil.getResourceSet().createResource(propURI);
            propResource.getContents().add(property);
            propResource.getContents().add(property.getItem());
            propResource.getContents().add(property.getItem().getState());
            EMFUtil.saveResource(propResource);
          }
 else {
            log.warn("String_Node_Str" + modelElement.getName() + "String_Node_Str");
          }
        }
 else {
          log.warn("String_Node_Str" + eObject.toString());
        }
      }
    }
  }
  emfUtil=null;
  return true;
}

Fixed version (ground truth):
@Override protected boolean doExecute() throws Exception {
  EMFUtil emfUtil=new EMFUtil();
  for (  File file : fileList) {
    if (file.isFile()) {
      URI uri=URI.createFileURI(file.getAbsolutePath());
      Resource resource=emfUtil.getResourceSet().getResource(uri,true);
      EObject eObject=resource.getContents().get(0);
      if (FactoriesUtil.isProvFile(uri.fileExtension())) {
        for (        EObject object : resource.getContents()) {
          if (object instanceof Connection) {
            eObject=object;
            break;
          }
        }
      }
      if (eObject != null) {
        if (eObject instanceof ModelElement) {
          ModelElement modelElement=(ModelElement)eObject;
          AElementPersistance writer=ElementWriterFactory.getInstance().create(uri.fileExtension());
          Property oldPropery=PropertyHelper.getProperty(modelElement);
          if (writer != null) {
            Property property=writer.initProperty(modelElement);
            if (oldPropery != null) {
              property.setAuthor(oldPropery.getAuthor());
              property.getItem().setState(oldPropery.getItem().getState());
            }
            computePath(property,file);
            URI propURI=resource.getURI().trimFileExtension().appendFileExtension(FactoriesUtil.PROPERTIES_EXTENSION);
            Resource propResource=emfUtil.getResourceSet().createResource(propURI);
            propResource.getContents().add(property);
            propResource.getContents().add(property.getItem());
            propResource.getContents().add(property.getItem().getState());
            EMFUtil.saveResource(propResource);
          }
 else {
            log.warn("String_Node_Str" + modelElement.getName() + "String_Node_Str");
          }
        }
 else {
          log.warn("String_Node_Str" + eObject.toString());
        }
      }
    }
  }
  emfUtil=null;
  return true;
}