Maved the PHP code to the php/ subdirectory.

Nyaatori is NOT going to be a PHP only project; eventually it will allow
the creation of websites with different languages. (This is only a part
of the cool goodness of having all of the transformation done on XSLT)

So, I added GluePHP to handle the Controller part of the PHP
mini-framework.
markdown.php is gone.

While I think everybody should use it, I realized this is not part
of the framework, and therefore it had to be removed.