Program: 1825
Project: 1825
Buggy source:
@Command(aliases="String_Node_Str",usage="String_Node_Str",desc="String_Node_Str",modifiers={"String_Node_Str","String_Node_Str"},flags="String_Node_Str",min=1) @CommandPermissions("String_Node_Str") public static void addFlag(CommandContext args,Player player,HumanNPC npc){
  if (!args.hasFlag('a') && !args.hasFlag('g') && !args.hasFlag('m')&& !args.hasFlag('p')) {
    player.sendMessage(ChatColor.GRAY + "String_Node_Str");
    return;
  }
  Guard guard=npc.getType("String_Node_Str");
  int flagOffset=1, priority=1;
  if (args.hasFlag('i')) {
    ++flagOffset;
    priority=args.getInteger(1);
  }
  boolean isSafe=args.getString(flagOffset).charAt(0) == '-';
  if (args.hasFlag('a')) {
    guard.getFlags().addToAll(args.getFlags(),FlagInfo.newInstance("String_Node_Str",priority,isSafe));
  }
 else   if (args.argsLength() == 1 || flagOffset == 2) {
    player.sendMessage(ChatColor.GRAY + "String_Node_Str");
    return;
  }
  String name=isSafe ? args.getJoinedStrings(flagOffset).replaceFirst("String_Node_Str","String_Node_Str") : args.getJoinedStrings(flagOffset);
  name=name.toLowerCase();
  FlagType type=FlagType.PLAYER;
  if (args.hasFlag('g')) {
    if (!PermissionManager.useSuperPerms()) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    Group group=PermissionManager.getGroup(name);
    if (group == null) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    type=FlagType.GROUP;
  }
  if (args.hasFlag('m')) {
    if (!EntityUtils.validType(name,true)) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    type=FlagType.MOB;
  }
  String prefix=guard.getFlags().contains(type,name) ? "String_Node_Str" : "String_Node_Str";
  guard.getFlags().addFlag(type,FlagInfo.newInstance(name,priority,isSafe));
  player.sendMessage(ChatColor.GREEN + prefix + "String_Node_Str"+ StringUtils.wrap(name)+ "String_Node_Str");
}

Fixed version (ground truth):
@Command(aliases="String_Node_Str",usage="String_Node_Str",desc="String_Node_Str",modifiers={"String_Node_Str","String_Node_Str"},flags="String_Node_Str",min=1) @CommandPermissions("String_Node_Str") public static void addFlag(CommandContext args,Player player,HumanNPC npc){
  if (!args.hasFlag('a') && !args.hasFlag('g') && !args.hasFlag('m')&& !args.hasFlag('p')) {
    player.sendMessage(ChatColor.GRAY + "String_Node_Str");
    return;
  }
  Guard guard=npc.getType("String_Node_Str");
  int flagOffset=1, priority=1;
  if (args.hasFlag('i')) {
    ++flagOffset;
    priority=args.getInteger(1);
  }
  if (args.hasFlag('a')) {
    guard.getFlags().addToAll(args.getFlags(),FlagInfo.newInstance("String_Node_Str",priority,args.argsLength() > flagOffset ? args.getString(flagOffset).charAt(0) == '-' : false));
    player.sendMessage(ChatColor.GREEN + "String_Node_Str");
    return;
  }
 else   if (args.argsLength() == 1 || flagOffset == 2) {
    player.sendMessage(ChatColor.GRAY + "String_Node_Str");
    return;
  }
  boolean isSafe=args.getString(flagOffset).charAt(0) == '-';
  String name=isSafe ? args.getJoinedStrings(flagOffset).replaceFirst("String_Node_Str","String_Node_Str") : args.getJoinedStrings(flagOffset);
  name=name.toLowerCase();
  FlagType type=FlagType.PLAYER;
  if (args.hasFlag('g')) {
    if (!PermissionManager.useSuperPerms()) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    Group group=PermissionManager.getGroup(name);
    if (group == null) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    type=FlagType.GROUP;
  }
  if (args.hasFlag('m')) {
    if (!EntityUtils.validType(name,true)) {
      player.sendMessage(ChatColor.GRAY + "String_Node_Str");
      return;
    }
    type=FlagType.MOB;
  }
  String prefix=guard.getFlags().contains(type,name) ? "String_Node_Str" : "String_Node_Str";
  guard.getFlags().addFlag(type,FlagInfo.newInstance(name,priority,isSafe));
  player.sendMessage(ChatColor.GREEN + prefix + "String_Node_Str"+ StringUtils.wrap(name)+ "String_Node_Str");
}