He means, there are other files in the Package of PHPBB port from Toms' that you need to upload as well.
Some you will overwrite your existing Nuke files. All the files/folders in the HTML folder.

Just go through each directory one at a time and open each to see what files are in them. Then look at your FTP, the FIle/Directory structure is the same

Notice in the pic. I have the phpBB port files on the left and my root of my FTP on the right. Notice some folders on the right match ones on the left. Open each matching folder and copy the files within each over to it's matching folder/directory.
Some folders have sub-folders, so check carefully.