Program: 32572
Project: 32572
Buggy source:
@Override public void execute(CommandSender sender,String[] args){
  MessagesConfig messages=Messages.getInstance();
  Player player=(Player)sender;
  User user=User.get(player);
  if (!user.hasGuild()) {
    player.sendMessage(messages.generalHasNoGuild);
    return;
  }
  if (!user.isOwner()) {
    player.sendMessage(messages.generalIsNotOwner);
    return;
  }
  Guild guild=user.getGuild();
  List<InvitationList.Invitation> invitations=InvitationList.getInvitationsFor(guild);
  if (args.length < 1) {
    if (invitations.size() == 0) {
      player.sendMessage(messages.allyHasNotInvitation);
      return;
    }
    List<String> list=messages.allyInvitationList;
    String guildNames=StringUtils.toString(InvitationList.getInvitationGuildNames(guild),false);
    for (    String msg : list) {
      player.sendMessage(msg.replace("String_Node_Str",guildNames));
    }
    return;
  }
  String tag=args[0];
  if (!GuildUtils.tagExists(tag)) {
    player.sendMessage(StringUtils.replace(messages.generalGuildNotExists,"String_Node_Str",tag));
    return;
  }
  Guild invitedGuild=GuildUtils.byTag(tag);
  if (guild.equals(invitedGuild)) {
    player.sendMessage(messages.allySame);
    return;
  }
  if (guild.getAllies().contains(invitedGuild)) {
    player.sendMessage(messages.allyAlly);
    return;
  }
  if (InvitationList.hasInvitationFrom(guild,invitedGuild)) {
    if (!SimpleEventHandler.handle(new GuildAcceptAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
      return;
    }
    InvitationList.expireInvitation(invitedGuild,guild);
    guild.addAlly(invitedGuild);
    invitedGuild.addAlly(guild);
    player.sendMessage(StringUtils.replace(messages.allyDone,"String_Node_Str",invitedGuild.getName()));
    Player owner=invitedGuild.getOwner().getPlayer();
    if (owner != null) {
      owner.sendMessage(messages.allyIDone.replace("String_Node_Str",guild.getName()));
    }
    for (    User u : guild.getMembers()) {
      IndependentThread.action(ActionType.PREFIX_UPDATE_GUILD,u,invitedGuild);
    }
    for (    User u : invitedGuild.getMembers()) {
      IndependentThread.action(ActionType.PREFIX_UPDATE_GUILD,u,guild);
    }
    return;
  }
  if (InvitationList.hasInvitationFrom(invitedGuild,guild)) {
    if (!SimpleEventHandler.handle(new GuildRevokeAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
      return;
    }
    InvitationList.expireInvitation(guild,invitedGuild);
    player.sendMessage(messages.allyReturn.replace("String_Node_Str",invitedGuild.getName()));
    Player owner=invitedGuild.getOwner().getPlayer();
    if (owner != null) {
      owner.sendMessage(messages.allyIReturn.replace("String_Node_Str",guild.getName()));
    }
    return;
  }
  if (!SimpleEventHandler.handle(new GuildSendAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
    return;
  }
  InvitationList.createInvitation(guild,invitedGuild);
  player.sendMessage(messages.allyInviteDone.replace("String_Node_Str",invitedGuild.getName()));
  Player owner=invitedGuild.getOwner().getPlayer();
  if (owner != null) {
    owner.sendMessage(messages.allyToInvited.replace("String_Node_Str",guild.getName()));
  }
}

Fixed version (ground truth):
@Override public void execute(CommandSender sender,String[] args){
  MessagesConfig messages=Messages.getInstance();
  Player player=(Player)sender;
  User user=User.get(player);
  if (!user.hasGuild()) {
    player.sendMessage(messages.generalHasNoGuild);
    return;
  }
  if (!user.isOwner()) {
    player.sendMessage(messages.generalIsNotOwner);
    return;
  }
  Guild guild=user.getGuild();
  List<InvitationList.Invitation> invitations=InvitationList.getInvitationsFor(guild);
  if (args.length < 1) {
    if (invitations.size() == 0) {
      player.sendMessage(messages.allyHasNotInvitation);
      return;
    }
    List<String> list=messages.allyInvitationList;
    String guildNames=StringUtils.toString(InvitationList.getInvitationGuildNames(guild),false);
    for (    String msg : list) {
      player.sendMessage(msg.replace("String_Node_Str",guildNames));
    }
    return;
  }
  String tag=args[0];
  if (!GuildUtils.tagExists(tag)) {
    player.sendMessage(StringUtils.replace(messages.generalGuildNotExists,"String_Node_Str",tag));
    return;
  }
  Guild invitedGuild=GuildUtils.getByTag(tag);
  if (guild.equals(invitedGuild)) {
    player.sendMessage(messages.allySame);
    return;
  }
  if (guild.getAllies().contains(invitedGuild)) {
    player.sendMessage(messages.allyAlly);
    return;
  }
  if (InvitationList.hasInvitationFrom(guild,invitedGuild)) {
    if (!SimpleEventHandler.handle(new GuildAcceptAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
      return;
    }
    InvitationList.expireInvitation(invitedGuild,guild);
    guild.addAlly(invitedGuild);
    invitedGuild.addAlly(guild);
    player.sendMessage(StringUtils.replace(messages.allyDone,"String_Node_Str",invitedGuild.getName()));
    Player owner=invitedGuild.getOwner().getPlayer();
    if (owner != null) {
      owner.sendMessage(messages.allyIDone.replace("String_Node_Str",guild.getName()));
    }
    for (    User u : guild.getMembers()) {
      IndependentThread.action(ActionType.PREFIX_UPDATE_GUILD,u,invitedGuild);
    }
    for (    User u : invitedGuild.getMembers()) {
      IndependentThread.action(ActionType.PREFIX_UPDATE_GUILD,u,guild);
    }
    return;
  }
  if (InvitationList.hasInvitationFrom(invitedGuild,guild)) {
    if (!SimpleEventHandler.handle(new GuildRevokeAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
      return;
    }
    InvitationList.expireInvitation(guild,invitedGuild);
    player.sendMessage(messages.allyReturn.replace("String_Node_Str",invitedGuild.getName()));
    Player owner=invitedGuild.getOwner().getPlayer();
    if (owner != null) {
      owner.sendMessage(messages.allyIReturn.replace("String_Node_Str",guild.getName()));
    }
    return;
  }
  if (!SimpleEventHandler.handle(new GuildSendAllyInvitationEvent(EventCause.USER,user,guild,invitedGuild))) {
    return;
  }
  InvitationList.createInvitation(guild,invitedGuild);
  player.sendMessage(messages.allyInviteDone.replace("String_Node_Str",invitedGuild.getName()));
  Player owner=invitedGuild.getOwner().getPlayer();
  if (owner != null) {
    owner.sendMessage(messages.allyToInvited.replace("String_Node_Str",guild.getName()));
  }
}