Program: 138659
Project: 138659
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());
      EObject eObject=null;
      try {
        Resource resource=emfUtil.getResourceSet().getResource(uri,true);
        eObject=resource.getContents().get(0);
        if (FactoriesUtil.isProvFile(uri.fileExtension())) {
          for (          EObject object : resource.getContents()) {
            if (object instanceof Connection) {
              eObject=object;
              break;
            }
          }
        }
      }
 catch (      Exception e) {
        log.warn("String_Node_Str" + file.getAbsolutePath(),e);
      }
      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.setId(oldPropery.getId());
              property.setAuthor(oldPropery.getAuthor());
              property.getItem().setState(oldPropery.getItem().getState());
            }
            if (file.getName().endsWith("String_Node_Str")) {
              System.out.println("String_Node_Str");
            }
            String statePathStr=PropertyHelper.computePath(property,file);
            property.getItem().getState().setPath(statePathStr);
            URI propURI=uri.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 {
  boolean ok=true;
  EMFUtil emfUtil=new EMFUtil();
  for (  File file : fileList) {
    if (file.isFile()) {
      URI uri=URI.createFileURI(file.getAbsolutePath());
      if (log.isDebugEnabled()) {
        log.debug("String_Node_Str" + uri.toString());
      }
      EObject eObject=null;
      try {
        Resource resource=emfUtil.getResourceSet().getResource(uri,true);
        eObject=resource.getContents().get(0);
        if (FactoriesUtil.isProvFile(uri.fileExtension())) {
          for (          EObject object : resource.getContents()) {
            if (object instanceof Connection) {
              eObject=object;
              break;
            }
          }
        }
      }
 catch (      Exception e) {
        log.warn("String_Node_Str" + file.getAbsolutePath(),e);
        ok=false;
      }
      if (eObject != null) {
        if (eObject instanceof ModelElement) {
          try {
            saveObject(emfUtil,file,uri,eObject);
          }
 catch (          Exception e) {
            log.error("String_Node_Str" + eObject + "String_Node_Str"+ file+ "String_Node_Str"+ uri,e);
            ok=false;
          }
        }
 else {
          log.warn("String_Node_Str" + eObject.toString());
          ok=false;
        }
      }
    }
  }
  emfUtil=null;
  return ok;
}