Program: 151817
Project: 151817
Buggy source:
public void execute(Player player,String message){
  String[] arguments=extractArguments(message);
  if (arguments.length > 0) {
    String prefix=commandPrefix();
    String commandName=arguments[0];
    if (!commandName.startsWith(prefix)) {
      commandName=prefix + commandName;
    }
    PlayerCommand command=parser.getPlayerCommand(commandName);
    player.addMessage(command.getHelpText(prefix));
    List<String> aliases=player.getServer().config.commands.get(command.getName()).aliases;
    if (!aliases.isEmpty()) {
      StringBuffer line=new StringBuffer();
      for (      String alias : aliases) {
        line.append(commandPrefix());
        line.append(alias);
        line.append("String_Node_Str");
      }
      player.addTCaptionedMessage("String_Node_Str",line.toString());
    }
  }
 else {
    List<PermissionContainer> containers=player.getServer().config.containers(player.position());
    Set<CommandConfig> commands=new TreeSet<CommandConfig>();
    for (    PermissionContainer container : containers) {
      for (      CommandConfig command : container.commands) {
        if (command.allow.contains(player)) {
          commands.add(command);
        }
      }
    }
    StringBuffer line=new StringBuffer();
    String prefix=commandPrefix();
    for (    CommandConfig cmd : commands) {
      Command command=parser.getPlayerCommand(cmd.originalName);
      if (cmd.hidden || command.hidden()) {
        continue;
      }
      line.append(prefix);
      line.append(cmd.name);
      line.append("String_Node_Str");
    }
    player.addTCaptionedMessage("String_Node_Str",line.toString());
    player.addTMessage(Color.GRAY,"String_Node_Str",prefix + "String_Node_Str");
    String[] helplines=player.getServer().helptext.getHelpText().split("String_Node_Str");
    if (helplines.length > 0) {
      player.addMessage("String_Node_Str");
      for (      String l : helplines) {
        player.addMessage(Color.WHITE,l);
      }
    }
  }
}

Fixed version (ground truth):
public void execute(Player player,String message){
  String[] arguments=extractArguments(message);
  if (arguments.length > 0) {
    String prefix=commandPrefix();
    String commandName=arguments[0];
    if (!commandName.startsWith(prefix)) {
      commandName=prefix + commandName;
    }
    PlayerCommand command=parser.getPlayerCommand(commandName);
    player.addMessage(command.getHelpText(prefix));
    List<String> aliases=player.getServer().config.commands.get(command.getName()).aliases;
    if (aliases != null) {
      StringBuffer line=new StringBuffer();
      for (      String alias : aliases) {
        line.append(commandPrefix());
        line.append(alias);
        line.append("String_Node_Str");
      }
      player.addTCaptionedMessage("String_Node_Str",line.toString());
    }
  }
 else {
    List<PermissionContainer> containers=player.getServer().config.containers(player.position());
    Set<CommandConfig> commands=new TreeSet<CommandConfig>();
    for (    PermissionContainer container : containers) {
      for (      CommandConfig command : container.commands) {
        if (command.allow.contains(player)) {
          commands.add(command);
        }
      }
    }
    StringBuffer line=new StringBuffer();
    String prefix=commandPrefix();
    for (    CommandConfig cmd : commands) {
      Command command=parser.getPlayerCommand(cmd.originalName);
      System.out.println(cmd.name);
      if (cmd.hidden || (command != null && command.hidden())) {
        continue;
      }
      line.append(prefix);
      line.append(cmd.name);
      line.append("String_Node_Str");
    }
    player.addTCaptionedMessage("String_Node_Str",line.toString());
    player.addTMessage(Color.GRAY,"String_Node_Str",prefix + "String_Node_Str");
    String[] helplines=player.getServer().helptext.getHelpText().split("String_Node_Str");
    if (helplines.length > 0) {
      player.addMessage("String_Node_Str");
      for (      String l : helplines) {
        player.addMessage(Color.WHITE,l);
      }
    }
  }
}