I'm happy to say that my previous post about using a modern version of MooTools in Joomla no longer applies. With the latest update to Joomla (1.5.20) a new plugin was added, providing MooTools 1.2.4, with backwards compatibility for Joomla extensions that relied on MooTools 1.1. This update came just in time for me as I was updating a client's site from Joomla 1.0 and had a lot of Javascript to rewrite with new dependencies and conflicts to avoid.
For upgrade installs, this plugin is not enabled by default.
If you had followed my previous method, then you simply need to remove the code you added to your template's index.php, and enable the new Mootools Upgrade plugin through the Joomla Extension manager.
I have run into at least one situation where the new Mootools was required, but Joomla wasn't including it on certain pages. To force Joomla to included MooTools throughout your entire template, simply add the following code to your index.php:
JHTML::_('behavior.mootools');
This triggers Joomla to include the MooTools javascript library on your page, even if a component or module isn't calling for it.
