Program: 187582
Project: 187582
Buggy source:
public boolean onCommand(CommandSender sender,Command command,String label,String[] args){
  if (sender instanceof Player) {
    Player player=(Player)sender;
    if (args.length == 1 && MyPetPermissions.has(player,"String_Node_Str") && MyPetList.hasMyPet(args[0])) {
      MyPet myPet=MyPetList.getMyPet(args[0]);
      if (myPet.getSkills().isSkillActive("String_Node_Str")) {
        ((Beacon)myPet.getSkills().getSkill("String_Node_Str")).activate(player);
      }
    }
 else     if (MyPetList.hasMyPet(player)) {
      MyPet myPet=MyPetList.getMyPet(player);
      if (myPet.status == PetState.Despawned) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.status == PetState.Dead) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName).replace("String_Node_Str","String_Node_Str" + myPet.respawnTime));
        return true;
      }
      if (args.length >= 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
        ((Beacon)myPet.getSkills().getSkill("String_Node_Str")).stop(true);
        return true;
      }
      if (player.getGameMode() == GameMode.CREATIVE && !MyPetPermissions.has(player,"String_Node_Str")) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getSkills().hasSkill("String_Node_Str")) {
        myPet.getSkills().getSkill("String_Node_Str").activate();
      }
    }
 else {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
  }
  return true;
}

Fixed version (ground truth):
public boolean onCommand(CommandSender sender,Command command,String label,String[] args){
  if (sender instanceof Player) {
    Player player=(Player)sender;
    if (args.length == 1 && MyPetPermissions.has(player,"String_Node_Str") && MyPetList.hasMyPet(args[0])) {
      MyPet myPet=MyPetList.getMyPet(args[0]);
      if (myPet.getSkills().isSkillActive("String_Node_Str")) {
        ((Beacon)myPet.getSkills().getSkill("String_Node_Str")).activate(player);
      }
    }
 else     if (MyPetList.hasMyPet(player)) {
      MyPet myPet=MyPetList.getMyPet(player);
      if (!MyPetPermissions.hasExtended(player,"String_Node_Str")) {
        myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
      if (myPet.status == PetState.Despawned) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.status == PetState.Dead) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName).replace("String_Node_Str","String_Node_Str" + myPet.respawnTime));
        return true;
      }
      if (args.length >= 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
        ((Beacon)myPet.getSkills().getSkill("String_Node_Str")).stop(true);
        return true;
      }
      if (player.getGameMode() == GameMode.CREATIVE && !MyPetPermissions.has(player,"String_Node_Str")) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getSkills().hasSkill("String_Node_Str")) {
        myPet.getSkills().getSkill("String_Node_Str").activate();
      }
    }
 else {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
  }
  return true;
}