I think the easiest way to do this (especially since you may not have access to the apache config files, just .htaccess) is to use the Files directive and ForceType
<Files articles>
ForceType application/x-httpd-php
</Files>
http://domainname.com/articles/whatever will just be parsed (same page) as http://domainname.com/articles.
If you have access to the apache config files, I believe you can use the Location directive to stipulate the virtual root...
I suppose I should point out that you have to have a file called "articles" in the example with the Files directive. Zend Studio can be configured to read a no extension file as a PHP file. Also, you can create an articles.php file (for updating/writing) and then just create a sym link like...
$ ln -s articles.php articles
Also, I dunno what type of Apache server Zend Studio implements. I can't debug in the browser unless I use remote debugging. What are you using?