Program: 98925
Project: 98925
Buggy source:
public boolean onCommand(CommandSender sender,Command command,String commandLabel,String[] args){
  String[] split=args;
  String commandName=command.getName().toLowerCase();
  if (sender instanceof Player) {
    Player player=(Player)sender;
    if (commandName.equals("String_Node_Str")) {
      if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.isAdmin(player)) {
        if (!warning) {
          player.sendMessage(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str");
          player.sendMessage("String_Node_Str");
          player.sendMessage("String_Node_Str" + ChatColor.RED + "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
          warning=true;
        }
 else {
          Converter.convert(player,getServer(),warpList);
          warning=false;
        }
      }
 else       if ((split.length == 1 || (split.length == 2 && isInteger(split[1]))) && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.list(player)) {
        Lister lister=new Lister(warpList);
        lister.addPlayer(player);
        if (split.length == 2) {
          int page=Integer.parseInt(split[1]);
          if (page < 1) {
            player.sendMessage(ChatColor.RED + "String_Node_Str");
            return true;
          }
 else           if (page > lister.getMaxPages(player)) {
            player.sendMessage(ChatColor.RED + "String_Node_Str" + lister.getMaxPages(player)+ "String_Node_Str");
            return true;
          }
          lister.setPage(page);
        }
 else {
          lister.setPage(1);
        }
        lister.list();
      }
 else       if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.list(player)) {
        warpList.list(player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.search(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        Searcher searcher=new Searcher(warpList);
        searcher.addPlayer(player);
        searcher.setQuery(name);
        searcher.search();
      }
 else       if (split.length > 1 && (split[0].equalsIgnoreCase("String_Node_Str") || split[0].equalsIgnoreCase("String_Node_Str")) && (WarpPermissions.publicCreate(player) || WarpPermissions.privateCreate(player))) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        if (WarpPermissions.publicCreate(player)) {
          warpList.addWarp(name,player);
        }
 else {
          warpList.addWarpPrivate(name,player);
        }
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.privateCreate(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.addWarpPrivate(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.delete(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.deleteWarp(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.welcome(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.welcomeMessage(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.canPrivate(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.privatize(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.canPublic(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.publicize(name,player);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.give(player)) {
        Player givee=getServer().getPlayer(split[1]);
        String giveeName=(givee == null) ? split[1] : givee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.give(name,player,giveeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.invite(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.invite(name,player,inviteeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.uninvite(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.uninvite(name,player,inviteeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.isAdmin(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.warpTo(name,invitee);
      }
 else       if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str")) {
        ArrayList<String> messages=new ArrayList<String>();
        messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.RED+ "String_Node_Str");
        if (WarpPermissions.warp(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.publicCreate(player) || WarpPermissions.privateCreate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.privateCreate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.delete(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.welcome(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.list(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.search(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.give(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.invite(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.uninvite(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.canPublic(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
        }
        if (WarpPermissions.canPrivate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
        }
        for (        String message : messages) {
          player.sendMessage(message);
        }
      }
 else       if (split.length > 0 && WarpPermissions.warp(player)) {
        String name="String_Node_Str";
        for (int i=0; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.warpTo(name,player);
      }
 else {
        return false;
      }
      return true;
    }
  }
  return false;
}

Fixed version (ground truth):
public boolean onCommand(CommandSender sender,Command command,String commandLabel,String[] args){
  String[] split=args;
  String commandName=command.getName().toLowerCase();
  if (sender instanceof Player) {
    Player player=(Player)sender;
    if (commandName.equals("String_Node_Str")) {
      if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.isAdmin(player)) {
        if (!warning) {
          player.sendMessage(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str");
          player.sendMessage("String_Node_Str");
          player.sendMessage("String_Node_Str" + ChatColor.RED + "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
          warning=true;
        }
 else {
          Converter.convert(player,getServer(),warpList);
          warning=false;
        }
      }
 else       if ((split.length == 1 || (split.length == 2 && isInteger(split[1]))) && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.list(player)) {
        Lister lister=new Lister(warpList);
        lister.addPlayer(player);
        if (split.length == 2) {
          int page=Integer.parseInt(split[1]);
          if (page < 1) {
            player.sendMessage(ChatColor.RED + "String_Node_Str");
            return true;
          }
 else           if (page > lister.getMaxPages(player)) {
            player.sendMessage(ChatColor.RED + "String_Node_Str" + lister.getMaxPages(player)+ "String_Node_Str");
            return true;
          }
          lister.setPage(page);
        }
 else {
          lister.setPage(1);
        }
        lister.list();
      }
 else       if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.list(player)) {
        warpList.list(player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.search(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        Searcher searcher=new Searcher(warpList);
        searcher.addPlayer(player);
        searcher.setQuery(name);
        searcher.search();
      }
 else       if (split.length > 1 && (split[0].equalsIgnoreCase("String_Node_Str") || split[0].equalsIgnoreCase("String_Node_Str")) && (WarpPermissions.publicCreate(player) || WarpPermissions.privateCreate(player))) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        if (WarpPermissions.publicCreate(player)) {
          warpList.addWarp(name,player);
        }
 else {
          warpList.addWarpPrivate(name,player);
        }
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.compass(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.point(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.privateCreate(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.addWarpPrivate(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.delete(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.deleteWarp(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.welcome(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.welcomeMessage(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.canPrivate(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.privatize(name,player);
      }
 else       if (split.length > 1 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.canPublic(player)) {
        String name="String_Node_Str";
        for (int i=1; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.publicize(name,player);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.give(player)) {
        Player givee=getServer().getPlayer(split[1]);
        String giveeName=(givee == null) ? split[1] : givee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.give(name,player,giveeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.invite(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.invite(name,player,inviteeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.uninvite(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.uninvite(name,player,inviteeName);
      }
 else       if (split.length > 2 && split[0].equalsIgnoreCase("String_Node_Str") && WarpPermissions.isAdmin(player)) {
        Player invitee=getServer().getPlayer(split[1]);
        String inviteeName=(invitee == null) ? split[1] : invitee.getName();
        String name="String_Node_Str";
        for (int i=2; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.warpTo(name,invitee);
      }
 else       if (split.length == 1 && split[0].equalsIgnoreCase("String_Node_Str")) {
        ArrayList<String> messages=new ArrayList<String>();
        messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.RED+ "String_Node_Str");
        if (WarpPermissions.warp(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.publicCreate(player) || WarpPermissions.privateCreate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.privateCreate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.delete(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.welcome(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.list(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.search(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.give(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.invite(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.uninvite(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str");
        }
        if (WarpPermissions.canPublic(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
        }
        if (WarpPermissions.canPrivate(player)) {
          messages.add(ChatColor.RED + "String_Node_Str" + ChatColor.WHITE+ "String_Node_Str"+ ChatColor.GRAY+ "String_Node_Str"+ ChatColor.WHITE+ "String_Node_Str");
        }
        for (        String message : messages) {
          player.sendMessage(message);
        }
      }
 else       if (split.length > 0 && WarpPermissions.warp(player)) {
        String name="String_Node_Str";
        for (int i=0; i < split.length; i++) {
          name+=split[i];
          if (i + 1 < split.length)           name+="String_Node_Str";
        }
        warpList.warpTo(name,player);
      }
 else {
        return false;
      }
      return true;
    }
  }
  return false;
}