Program: 58118
Project: 58118
Buggy source:
@Override public boolean onCommand(CommandSender sender,Command cmd,String commandLabel,String[] args){
  Player player;
  if (sender instanceof Player) {
    player=(Player)sender;
  }
 else {
    player=null;
  }
  if (PlotMain.hasPermission(player,"String_Node_Str")) {
    return no_permission(player);
  }
  if ((args.length < 1) || ((args.length >= 1) && (args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")))) {
    if (args.length < 2) {
      StringBuilder builder=new StringBuilder();
      builder.append(C.HELP_INFO.s());
      for (      SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
        builder.append("String_Node_Str" + C.HELP_INFO_ITEM.s().replaceAll("String_Node_Str",category.toString().toLowerCase()).replaceAll("String_Node_Str",category.toString()));
      }
      PlayerFunctions.sendMessage(player,builder.toString());
      return true;
    }
    String cat=args[1];
    SubCommand.CommandCategory cato=null;
    for (    SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
      if (cat.equalsIgnoreCase(category.toString())) {
        cato=category;
        break;
      }
    }
    if (cato == null) {
      StringBuilder builder=new StringBuilder();
      builder.append(C.HELP_INFO.s());
      for (      SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
        builder.append("String_Node_Str" + C.HELP_INFO_ITEM.s().replaceAll("String_Node_Str",category.toString().toLowerCase()).replaceAll("String_Node_Str",category.toString()));
      }
      PlayerFunctions.sendMessage(player,builder.toString());
      return true;
    }
    StringBuilder help=new StringBuilder();
    for (    String string : helpMenu(player,cato)) {
      help.append(string + "String_Node_Str");
    }
    PlayerFunctions.sendMessage(player,help.toString());
    return true;
  }
 else {
    for (    SubCommand command : subCommands) {
      if (command.cmd.equalsIgnoreCase(args[0]) || command.alias.equalsIgnoreCase(args[0])) {
        String[] arguments=new String[args.length - 1];
        for (int x=1; x < args.length; x++) {
          arguments[x - 1]=args[x];
        }
        if (command.permission.hasPermission(player)) {
          if (player != null || !command.isPlayer) {
            return command.execute(player,arguments);
          }
 else {
            PlayerFunctions.sendMessage(player,C.IS_CONSOLE);
            return false;
          }
        }
 else {
          return no_permission(player);
        }
      }
    }
    PlayerFunctions.sendMessage(player,C.NOT_VALID_SUBCOMMAND);
  }
  return false;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandSender sender,Command cmd,String commandLabel,String[] args){
  Player player;
  if (sender instanceof Player) {
    player=(Player)sender;
  }
 else {
    player=null;
  }
  if (!PlotMain.hasPermission(player,"String_Node_Str")) {
    return no_permission(player);
  }
  if ((args.length < 1) || ((args.length >= 1) && (args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")))) {
    if (args.length < 2) {
      StringBuilder builder=new StringBuilder();
      builder.append(C.HELP_INFO.s());
      for (      SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
        builder.append("String_Node_Str" + C.HELP_INFO_ITEM.s().replaceAll("String_Node_Str",category.toString().toLowerCase()).replaceAll("String_Node_Str",category.toString()));
      }
      PlayerFunctions.sendMessage(player,builder.toString());
      return true;
    }
    String cat=args[1];
    SubCommand.CommandCategory cato=null;
    for (    SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
      if (cat.equalsIgnoreCase(category.toString())) {
        cato=category;
        break;
      }
    }
    if (cato == null) {
      StringBuilder builder=new StringBuilder();
      builder.append(C.HELP_INFO.s());
      for (      SubCommand.CommandCategory category : SubCommand.CommandCategory.values()) {
        builder.append("String_Node_Str" + C.HELP_INFO_ITEM.s().replaceAll("String_Node_Str",category.toString().toLowerCase()).replaceAll("String_Node_Str",category.toString()));
      }
      PlayerFunctions.sendMessage(player,builder.toString());
      return true;
    }
    StringBuilder help=new StringBuilder();
    for (    String string : helpMenu(player,cato)) {
      help.append(string + "String_Node_Str");
    }
    PlayerFunctions.sendMessage(player,help.toString());
    return true;
  }
 else {
    for (    SubCommand command : subCommands) {
      if (command.cmd.equalsIgnoreCase(args[0]) || command.alias.equalsIgnoreCase(args[0])) {
        String[] arguments=new String[args.length - 1];
        for (int x=1; x < args.length; x++) {
          arguments[x - 1]=args[x];
        }
        if (command.permission.hasPermission(player)) {
          if (player != null || !command.isPlayer) {
            return command.execute(player,arguments);
          }
 else {
            PlayerFunctions.sendMessage(player,C.IS_CONSOLE);
            return false;
          }
        }
 else {
          return no_permission(player);
        }
      }
    }
    PlayerFunctions.sendMessage(player,C.NOT_VALID_SUBCOMMAND);
  }
  return false;
}