Just edit the head.phtml located at here:
Open it and you should see the entire HTML header that Magento uses to render all pages of your store. Simply add a hard coded line of script tag anywhere appropriate:
<?xml version="1.0"?> <layout version="1.1.1"> <default> <reference name="head"> <action method="removeItem"><type>js</type><name>prototype/prototype.js</name></action> </reference> </default> </layout>
Refresh your store’s cache and you should see no local prototype/prototype.js being loaded in the HTMl header any more.