Yeap, that would be it. Infact, you can test it real quick, see if it works...
Place into /core/classes:
https://github.com/nshahzad/phpVMS/raw/master/core/classes/CodonRewrite.class.php
Then in the root (next to index.php), place in a .htaccess file:
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L]
See if that works. I can't edit the CodonRewrite file due to a permissions error, and he hasn't gotten back to me yet.