So would it be safe to simply change the pages directory to root?
No, as you will have to change the access rights to your WB root so that WB can write the files. (See above.) This is why it's a bad idea.
also, what happens if I change the page extention to nothing?
The Web server will no longer execute the files as PHP, but show them as plain text. This is not what you're after.
@WebBird - my htaccess file is the code in my older post, and even with that in place, all the links on my site show up as full URLs, and when you click them, they lead you to the complete URL
The .htaccess means that you can put something like
into your browser address line and get the page
in return. So you can use short URLs in Mails etc. But WB itself will still use the "correct" (long) URLs in the nav menus etc. To change that, you will have to edit the Frontend class as you did above.
In any case, this is a very dirty hack (you will loose when upgrading WB to a newer version), so you may think about it again.
What's so bad with /pages/?