Program: 149385
Project: 149385
Buggy source:
public JSONObject updateInstance(JSONObject instance,JSONArray variables) throws IOException {
  if (variables != null && !variables.isEmpty()) {
    JSONArray instanceBoxes=instance.getJSONArray("String_Node_Str");
    JSONObject mainBox=instanceBoxes.getJSONObject(0);
    JSONArray boxStack=new BoxStack(mainBox.getString("String_Node_Str"),instanceBoxes,this).toJSONArray();
    JSONArray boxVariables=new JSONArray();
    for (    Object box : boxStack) {
      boxVariables.addAll(((JSONObject)box).getJSONArray("String_Node_Str"));
    }
    JSONArray instanceVariables=instance.getJSONArray("String_Node_Str");
    List<JSONObject> newVariables=new ArrayList<JSONObject>();
    for (    Object variable : variables) {
      JSONObject variableJson=(JSONObject)variable;
      JSONObject instanceVariable=findVariable(variableJson,instanceVariables);
      if (instanceVariable == null) {
        JSONObject boxVariable=findVariable(variableJson,boxVariables);
        if (boxVariable != null) {
          instanceVariable=JSONObject.fromObject(boxVariable);
          if (instanceVariable.getString("String_Node_Str").isEmpty()) {
            instanceVariable.remove("String_Node_Str");
          }
          newVariables.add(instanceVariable);
        }
      }
      if (instanceVariable != null) {
        instanceVariable.put("String_Node_Str",variableJson.getString("String_Node_Str"));
      }
    }
    instanceVariables.addAll(newVariables);
    instance.put("String_Node_Str",instanceVariables);
  }
  HttpPut put=new HttpPut(getInstanceUrl(instance.getString("String_Node_Str")));
  put.setEntity(new StringEntity(instance.toString(),ContentType.APPLICATION_JSON));
  try {
    HttpResponse response=execute(put);
    return JSONObject.fromObject(getResponseBodyAsString(response));
  }
  finally {
    put.reset();
  }
}

Fixed version (ground truth):
public JSONObject updateInstance(JSONObject instance,JSONArray variables,String boxVersion) throws IOException {
  JSONArray variablesWithFullScope=new JSONArray();
  if (variables != null && !variables.isEmpty()) {
    JSONArray instanceBoxes=instance.getJSONArray("String_Node_Str");
    JSONObject mainBox=instanceBoxes.getJSONObject(0);
    BoxStack boxStack=new BoxStack(mainBox.getString("String_Node_Str"),instanceBoxes,this);
    JSONArray stackBoxes=boxStack.toJSONArray();
    JSONObject boxVersionJson=boxStack.findBox(boxVersion);
    if (boxVersionJson == null) {
      throw new IOException(MessageFormat.format("String_Node_Str",instance.getString("String_Node_Str"),boxVersion));
    }
    boxVersion=boxVersionJson.getString("String_Node_Str");
    JSONArray boxVariables=null;
    for (    Object box : stackBoxes) {
      JSONObject boxJson=(JSONObject)box;
      if (boxJson.getString("String_Node_Str").equals(boxVersion)) {
        boxVariables=boxJson.getJSONArray("String_Node_Str");
        break;
      }
    }
    if (boxVariables == null) {
      throw new IOException(MessageFormat.format("String_Node_Str",instance.getString("String_Node_Str"),boxVersion));
    }
    if (!boxVariables.isEmpty()) {
      String boxScope=boxVariables.getJSONObject(0).getString("String_Node_Str");
      for (      Object variable : variables) {
        JSONObject variableWithFullScope=JSONObject.fromObject(variable);
        String scope=variableWithFullScope.containsKey("String_Node_Str") ? variableWithFullScope.getString("String_Node_Str") : StringUtils.EMPTY;
        if (!StringUtils.isBlank(boxScope)) {
          scope=StringUtils.isBlank(scope) ? boxScope : boxScope + '.' + scope;
        }
        variableWithFullScope.put("String_Node_Str",scope);
        variablesWithFullScope.add(variableWithFullScope);
      }
    }
 else     if (!variables.isEmpty()) {
      throw new IOException(MessageFormat.format("String_Node_Str",boxVersion));
    }
  }
  return updateInstance(instance,variablesWithFullScope);
}