Program: 1900
Project: 1900
Buggy source:
@Override public boolean onCommand(CommandSender sender,Command command,String commandLabel,String[] args){
  if (!(sender instanceof Player)) {
    sender.sendMessage(MessageUtils.mustBeIngameMessage);
    return true;
  }
  Player player=(Player)sender;
  HumanNPC npc=null;
  boolean returnval=false;
  if (NPCManager.validateSelected((Player)sender)) {
    npc=NPCManager.get(NPCManager.selectedNPCs.get(player.getName()));
  }
 else {
    sender.sendMessage(MessageUtils.mustHaveNPCSelectedMessage);
    return true;
  }
  if (!NPCManager.validateOwnership(player,npc.getUID())) {
    sender.sendMessage(MessageUtils.notOwnerMessage);
    return true;
  }
  if (!npc.isGuard()) {
    sender.sendMessage(ChatColor.RED + "String_Node_Str");
    return true;
  }
 else {
    if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canUse(player,npc,"String_Node_Str")) {
        HelpUtils.sendGuardHelp(sender);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        toggleBodyguard(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        toggleBouncer(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
    if (args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        addToBlacklist(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canUse(player,npc,"String_Node_Str")) {
        displayBlacklist(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        addToWhitelist(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canUse(player,npc,"String_Node_Str")) {
        displayWhitelist(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (npc.getGuard().isBouncer() && args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        setProtectionRadius(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (!npc.getGuard().isBouncer() && args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      sender.sendMessage(ChatColor.RED + "String_Node_Str");
    }
 else {
      sender.sendMessage(ChatColor.GRAY + "String_Node_Str");
    }
    PropertyManager.save(npc);
  }
  return returnval;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandSender sender,Command command,String commandLabel,String[] args){
  if (!(sender instanceof Player)) {
    sender.sendMessage(MessageUtils.mustBeIngameMessage);
    return true;
  }
  Player player=(Player)sender;
  HumanNPC npc=null;
  boolean returnval=false;
  if (NPCManager.validateSelected((Player)sender)) {
    npc=NPCManager.get(NPCManager.selectedNPCs.get(player.getName()));
  }
 else {
    sender.sendMessage(MessageUtils.mustHaveNPCSelectedMessage);
    return true;
  }
  if (!NPCManager.validateOwnership(player,npc.getUID())) {
    sender.sendMessage(MessageUtils.notOwnerMessage);
    return true;
  }
  if (!npc.isGuard()) {
    sender.sendMessage(ChatColor.RED + "String_Node_Str");
    return true;
  }
 else {
    if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canHelp(player,npc,"String_Node_Str")) {
        HelpUtils.sendGuardHelp(sender);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        toggleBodyguard(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        toggleBouncer(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
    if (args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        addToBlacklist(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canUse(player,npc,"String_Node_Str")) {
        displayBlacklist(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        addToWhitelist(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (args.length == 1 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canUse(player,npc,"String_Node_Str")) {
        displayWhitelist(player,npc);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (npc.getGuard().isBouncer() && args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      if (Permission.canModify(player,npc,"String_Node_Str")) {
        setProtectionRadius(player,npc,args[1]);
      }
 else {
        sender.sendMessage(MessageUtils.noPermissionsMessage);
      }
      returnval=true;
    }
 else     if (!npc.getGuard().isBouncer() && args.length == 2 && args[0].equalsIgnoreCase("String_Node_Str")) {
      sender.sendMessage(ChatColor.RED + "String_Node_Str");
    }
 else {
      sender.sendMessage(ChatColor.GRAY + "String_Node_Str");
    }
    PropertyManager.save(npc);
  }
  return returnval;
}