JQuery is an independent library, that can co-exist with other libraries like Anguila. Here some steps that enable a developer to use JQuery in a GUI extension.
1) Update your JQuery file to use the noConflict method and pass it to a variable called for instance $j.
2) Reference the updated JQuery file in a group of resources used by your GUI Extension.
3) Start using JQuery with the $j variable name or jQuery instead of $ which will be used for Anguila.
As a best practice when you have multiple GUI extensions that use JQuery, it does not make any sense to reference JQuery in each GUI Extension, in that case I would recommend to extend a Resources Group.
Using that approach we will have JQuery always available for all our GUI Extensions.