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We are actually using mostly JQuery in our former and current CMS products. Is it possible - and if how - to eliminate the mootools stuff and replace it with query so we will be able to reuse most of the code we have already in the old websites if we decide to transfer them to contao?
Sure there is. You have complete control over the output in the frontend so at the very least you are able to change the fe_page template and change whatever you might need. There are tutorials that use my first efforts to replace mootools. It is worth mentioning that Contao 3 has jQuery built in.
Tutorial: http://blog.qzminski.com/2010/03/how-to ... nd-jquery/
Also since the advent of Contao 3, within the Themes Layout, you have the option to tick a box to include the jQuery library in the layout. It also comes with jquery templates such as accordion.
So Contao can use both Mootools and jQuery without conflict.