Program: 187548
Project: 187548
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",false)) {
      Player petOwner=Bukkit.getServer().getPlayer(args[0]);
      if (petOwner == null || !petOwner.isOnline()) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
 else       if (!MyPetList.hasMyPet(petOwner)) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",petOwner.getName())));
        return true;
      }
      MyPet myPet=MyPetList.getMyPet(petOwner);
      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(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
      if (myPet.getStatus() == PetState.Despawned) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getStatus() == PetState.Dead) {
        sender.sendMessage(MyPetBukkitUtil.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",false)) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getSkills().hasSkill("String_Node_Str")) {
        ((ISkillActive)myPet.getSkills().getSkill("String_Node_Str")).activate();
      }
    }
 else {
      sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
    return true;
  }
  sender.sendMessage("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 && !args[0].equalsIgnoreCase("String_Node_Str") && MyPetPermissions.has(player,"String_Node_Str",false)) {
      Player petOwner=Bukkit.getServer().getPlayer(args[0]);
      if (petOwner == null || !petOwner.isOnline()) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
 else       if (!MyPetList.hasMyPet(petOwner)) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",petOwner.getName())));
        return true;
      }
      MyPet myPet=MyPetList.getMyPet(petOwner);
      if (myPet.getSkills().isSkillActive("String_Node_Str")) {
        ((Beacon)myPet.getSkills().getSkill("String_Node_Str")).activate(player);
      }
      return true;
    }
    if (MyPetList.hasMyPet(player)) {
      MyPet myPet=MyPetList.getMyPet(player);
      if (!MyPetPermissions.hasExtended(player,"String_Node_Str",true)) {
        myPet.sendMessageToOwner(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
      if (myPet.getStatus() == PetState.Despawned) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getStatus() == PetState.Dead) {
        sender.sendMessage(MyPetBukkitUtil.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",false)) {
        sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")).replace("String_Node_Str",myPet.petName));
        return true;
      }
      if (myPet.getSkills().hasSkill("String_Node_Str")) {
        ((ISkillActive)myPet.getSkills().getSkill("String_Node_Str")).activate();
      }
    }
 else {
      sender.sendMessage(MyPetBukkitUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
    return true;
  }
  sender.sendMessage("String_Node_Str");
  return true;
}