Program: 34942
Project: 34942
Buggy source:
public String add(String id,Boolean deffer,String prefix,String affix,Boolean withPkg){
  if (!contains(id)) {
    return id;
  }
  JSONObject node=map.getNode(id);
  if (node.containsKey("String_Node_Str") && "String_Node_Str".equals(node.getString("String_Node_Str"))) {
    deffer=false;
  }
  if (loaded.containsKey(id) && loaded.get(id) == deffer || deffer && loaded.containsKey(id) && !loaded.get(id)) {
    return getUri(id,true);
  }
 else   if (loaded.containsKey(id) && !deffer && loaded.get(id)) {
    remove(id,true);
  }
  Res item=new Res();
  item.setId(id);
  if (inspect) {
    if (stack.peek().getChildren() == null) {
      stack.peek().setChildren(new ArrayList<Res>());
    }
    stack.peek().getChildren().add(item);
    stack.add(item);
  }
  loaded.put(id,deffer);
  String pkg=(String)node.get("String_Node_Str");
  String uri=node.getString("String_Node_Str");
  if (withPkg && pkg != null) {
    JSONObject pkgNode=map.getNode(pkg,"String_Node_Str");
    uri=pkgNode.getString("String_Node_Str");
    if (pkgNode.containsKey("String_Node_Str")) {
      for (      Object dep : pkgNode.getJSONArray("String_Node_Str")) {
        loaded.put(dep.toString(),deffer);
        if (inspect) {
          Res has=new Res();
          has.setId(dep.toString());
          if (item.getChildren() == null) {
            item.setChildren(new ArrayList<Res>());
          }
          item.getChildren().add(has);
        }
      }
    }
  }
  if (node.containsKey("String_Node_Str")) {
    JSONArray deps=node.getJSONArray("String_Node_Str");
    for (    Object dep : deps) {
      this.add(dep.toString(),deffer,prefix,affix,withPkg);
    }
  }
  if (node.containsKey("String_Node_Str")) {
    JSONObject extras=node.getJSONObject("String_Node_Str");
    if (extras.containsKey("String_Node_Str")) {
      JSONArray async=node.getJSONArray("String_Node_Str");
      for (      Object dep : async) {
        this.add(dep.toString(),true,prefix,affix,withPkg);
      }
    }
  }
  if (inspect) {
    stack.pop();
  }
  String type=node.getString("String_Node_Str");
  if (!type.equals("String_Node_Str") && !type.equals("String_Node_Str")) {
    return getUri(id,true);
  }
  item.setUri(uri);
  item.setPrefix(prefix);
  item.setAffix(affix);
  item.setType(type);
  item.setAsync(deffer);
  res.add(item);
  return getUri(id,true);
}

Fixed version (ground truth):
public String add(String id,Boolean deffer,String prefix,String affix,Boolean withPkg){
  if (!contains(id)) {
    return id;
  }
  JSONObject node=map.getNode(id);
  if (node.containsKey("String_Node_Str") && "String_Node_Str".equals(node.getString("String_Node_Str"))) {
    deffer=false;
  }
  if (loaded.containsKey(id) && loaded.get(id) == deffer || deffer && loaded.containsKey(id) && !loaded.get(id)) {
    return getUri(id,true);
  }
 else   if (loaded.containsKey(id) && !deffer && loaded.get(id)) {
    remove(id,true);
  }
  Res item=new Res();
  item.setId(id);
  if (inspect) {
    if (stack.peek().getChildren() == null) {
      stack.peek().setChildren(new ArrayList<Res>());
    }
    stack.peek().getChildren().add(item);
    stack.add(item);
  }
  loaded.put(id,deffer);
  String pkg=(String)node.get("String_Node_Str");
  String uri=node.getString("String_Node_Str");
  if (withPkg && pkg != null) {
    JSONObject pkgNode=map.getNode(pkg,"String_Node_Str");
    uri=pkgNode.getString("String_Node_Str");
    if (pkgNode.containsKey("String_Node_Str")) {
      for (      Object dep : pkgNode.getJSONArray("String_Node_Str")) {
        loaded.put(dep.toString(),deffer);
        if (inspect) {
          Res has=new Res();
          has.setId(dep.toString());
          if (item.getChildren() == null) {
            item.setChildren(new ArrayList<Res>());
          }
          item.getChildren().add(has);
        }
      }
    }
  }
  if (node.containsKey("String_Node_Str")) {
    JSONArray deps=node.getJSONArray("String_Node_Str");
    for (    Object dep : deps) {
      this.add(dep.toString(),deffer,prefix,affix,withPkg);
    }
  }
  if (node.containsKey("String_Node_Str")) {
    JSONObject extras=node.getJSONObject("String_Node_Str");
    if (extras.containsKey("String_Node_Str")) {
      JSONArray async=extras.getJSONArray("String_Node_Str");
      for (      Object dep : async) {
        this.add(dep.toString(),true,prefix,affix,withPkg);
      }
    }
  }
  if (inspect) {
    stack.pop();
  }
  String type=node.getString("String_Node_Str");
  if (!type.equals("String_Node_Str") && !type.equals("String_Node_Str")) {
    return getUri(id,true);
  }
  item.setUri(uri);
  item.setPrefix(prefix);
  item.setAffix(affix);
  item.setType(type);
  item.setAsync(deffer);
  res.add(item);
  return getUri(id,true);
}