Hi both,
This is where we're stuck between a rock and a hard place…
Mootools was chosen for developing the portlet components (doclist, mySpaces, myTasks, etc.) due to it's very small footprint, excellent performance and ease of use; certainly when compared to the Prototype/Scriptaculous, Dojo and jQuery libraries at the time.
Other UI elements have been (and are currently being) updated to use the mootools library, as historically Alfresco has used somewhat of a mix of Yahoo, Dojo and in-house code which is a situation we'd like to get away from.
The problem with the Javascript Array object being extended is common to most frameworks - certainly using the heavyweight Prototype and Scriptaculous libraries won't make the issue go away. So we're stuck - we can't use jQuery throughout as it isn't as complete as Mootools and we don't like the bloat of Prototype/Scriptaculous.
The only thing I can suggest is that we can look again at jQuery for some of the more commonly extended web client UI, now they've mostly sorted out the dreadful performance issues. Mootools will still be used for the portlets and WCM UIs, but it shouldn't affect custom templates.
It would be useful to know which parts of the web client you need to be mootools-free before we start any investigative work.
Thanks,
Mike