Program: 187583
Project: 187583
Buggy source:
public boolean onCommand(CommandSender sender,Command command,String label,String[] args){
  if (sender instanceof Player) {
    Player petOwner=(Player)sender;
    if (MyPetList.hasMyPet(petOwner)) {
      MyPet myPet=MyPetList.getMyPet(petOwner);
      if (myPet.status == PetState.Despawned) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
 else       if (myPet.getSkills().hasSkill("String_Node_Str")) {
        Behavior behaviorSkill=(Behavior)myPet.getSkills().getSkill("String_Node_Str");
        if (args.length == 1) {
          if ((args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) && BehaviorState.Friendly.isActive()) {
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Friendly);
          }
 else           if ((args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) && BehaviorState.Aggressive.isActive()) {
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Aggressive);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str") && BehaviorState.Farm.isActive()) {
            behaviorSkill.activateBehavior(BehaviorState.Farm);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str") && BehaviorState.Raid.isActive()) {
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Raid);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str")) {
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Normal);
          }
 else {
            behaviorSkill.activate();
            return false;
          }
        }
 else {
          behaviorSkill.activate();
        }
      }
      return true;
    }
 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 petOwner=(Player)sender;
    if (MyPetList.hasMyPet(petOwner)) {
      MyPet myPet=MyPetList.getMyPet(petOwner);
      if (myPet.status == PetState.Despawned) {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
 else       if (myPet.getSkills().hasSkill("String_Node_Str")) {
        Behavior behaviorSkill=(Behavior)myPet.getSkills().getSkill("String_Node_Str");
        if (args.length == 1) {
          if ((args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) && BehaviorState.Friendly.isActive()) {
            if (!MyPetPermissions.hasExtended(petOwner,"String_Node_Str")) {
              myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
              return true;
            }
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Friendly);
          }
 else           if ((args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) && BehaviorState.Aggressive.isActive()) {
            if (!MyPetPermissions.hasExtended(petOwner,"String_Node_Str")) {
              myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
              return true;
            }
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Aggressive);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str") && BehaviorState.Farm.isActive()) {
            if (!MyPetPermissions.hasExtended(petOwner,"String_Node_Str")) {
              myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
              return true;
            }
            behaviorSkill.activateBehavior(BehaviorState.Farm);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str") && BehaviorState.Raid.isActive()) {
            if (!MyPetPermissions.hasExtended(petOwner,"String_Node_Str")) {
              myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
              return true;
            }
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Raid);
          }
 else           if (args[0].equalsIgnoreCase("String_Node_Str")) {
            behaviorSkill.activateBehavior(Behavior.BehaviorState.Normal);
          }
 else {
            behaviorSkill.activate();
            return false;
          }
        }
 else {
          behaviorSkill.activate();
        }
      }
      return true;
    }
 else {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
  }
  return true;
}