Program: 187584
Project: 187584
Buggy source:
public boolean onCommand(CommandSender sender,Command command,String label,String[] args){
  if (!(sender instanceof Player)) {
    return false;
  }
  Player player=(Player)sender;
  if (MyPetList.hasMyPet(player)) {
    MyPet myPet=MyPetList.getMyPet(player);
    if (MyPetConfig.automaticSkilltreeAssignment && !myPet.getOwner().isMyPetAdmin()) {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
 else     if (myPet.getSkillTree() != null && MyPetConfig.chooseSkilltreeOnce && !myPet.getOwner().isMyPetAdmin()) {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",myPet.petName)));
    }
 else     if (MyPetSkillTreeMobType.hasMobType(myPet.getPetType().getTypeName())) {
      MyPetSkillTreeMobType skillTreeMobType=MyPetSkillTreeMobType.getMobTypeByName(myPet.getPetType().getTypeName());
      if (args.length == 1) {
        if (skillTreeMobType.hasSkillTree(args[0])) {
          MyPetSkillTree skillTree=skillTreeMobType.getSkillTree(args[0]);
          if (MyPetPermissions.has(myPet.getOwner().getPlayer(),"String_Node_Str" + skillTree.getName())) {
            if (myPet.setSkilltree(skillTree)) {
              sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",skillTree.getName())));
            }
 else {
              sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
            }
          }
 else {
            sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",args[0])));
          }
        }
 else {
          sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",args[0])));
        }
      }
 else {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",myPet.petName)));
        for (        String skillTreeName : skillTreeMobType.getSkillTreeNames()) {
          if (MyPetPermissions.has(player,"String_Node_Str" + skillTreeName)) {
            sender.sendMessage("String_Node_Str" + skillTreeName);
          }
        }
      }
    }
  }
 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)) {
    return false;
  }
  Player player=(Player)sender;
  if (MyPetList.hasMyPet(player)) {
    MyPet myPet=MyPetList.getMyPet(player);
    if (MyPetConfig.automaticSkilltreeAssignment && !myPet.getOwner().isMyPetAdmin()) {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
    }
 else     if (myPet.getSkillTree() != null && MyPetConfig.chooseSkilltreeOnce && !myPet.getOwner().isMyPetAdmin()) {
      sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",myPet.petName)));
    }
 else     if (MyPetSkillTreeMobType.hasMobType(myPet.getPetType().getTypeName())) {
      if (!MyPetPermissions.hasExtended(player,"String_Node_Str")) {
        myPet.sendMessageToOwner(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
        return true;
      }
      MyPetSkillTreeMobType skillTreeMobType=MyPetSkillTreeMobType.getMobTypeByName(myPet.getPetType().getTypeName());
      if (args.length == 1) {
        if (skillTreeMobType.hasSkillTree(args[0])) {
          MyPetSkillTree skillTree=skillTreeMobType.getSkillTree(args[0]);
          if (MyPetPermissions.has(myPet.getOwner().getPlayer(),"String_Node_Str" + skillTree.getName())) {
            if (myPet.setSkilltree(skillTree)) {
              sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",skillTree.getName())));
            }
 else {
              sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
            }
          }
 else {
            sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",args[0])));
          }
        }
 else {
          sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",args[0])));
        }
      }
 else {
        sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str").replace("String_Node_Str",myPet.petName)));
        for (        String skillTreeName : skillTreeMobType.getSkillTreeNames()) {
          if (MyPetPermissions.has(player,"String_Node_Str" + skillTreeName)) {
            sender.sendMessage("String_Node_Str" + skillTreeName);
          }
        }
      }
    }
  }
 else {
    sender.sendMessage(MyPetUtil.setColors(MyPetLanguage.getString("String_Node_Str")));
  }
  return true;
}