Framework conflicts are a common problem people run into when using jQuery. While jQuery provides some tricks you can use to get around this, you may still run into issues when Joomla! generates MooTools effects. While writing the second edition of Learning Joomla! Extension Development, I decided to do a chapter on JavaScript and look into this problem a little bit more closely. It turns out you have to make sure MooTools loads before jQuery, then use one of the tricks detailed on jquery.com.
Fortunately, this can be done in Joomla! consistenly, so I documented it. Packt decided to release the entire JavaScript chapter as the sample PDF for my book, so you can read everything you need to know about implementing this technique for free!
