If you can alter index.html (or more likely index.php, right?) to use a different directory than /var/www/mollify/[client|server] for the scripts, move them out of the web tree entirely. I never leave any scripts in the web tree. My usual structure for sites looks like this:
So in your case I'd put the mollify directory under /var/www/include, but put the index.php file in /var/www/public or maybe in /var/www/public/mollify. Then I'd tell index.php to look in /var/www/include/mollify for the client and server directories.
/var/www/public contains index.php and other publicly-visible stuff
/var/www/include contains all the scripts accessed by index.php