Thought I'd share how I got it all working in the Asset Pipeline.
//= require jquery
//= require jquery_ujs
//= require bootstrap
//= require bootstrap-modalmanager
//= require bootstrap-modal
//= require jquery.easing
//= require jquery.cookie
//= require zeroclipboard
//= require jquery-1.9.0.min
//= require noconflict.jquery-1.9.0
//= require toggles
//= require jquery-1.10.1.min
//= require noconflict.jquery-1.10.1
//= require jquery.joyride-2.1
//= require jquery-1.7.2.min
//= require jquery-ui-1.8.7.custom.min
//= require noconflict.jquery-1.7.2
//= require jquery.inlineedit
//= require pubsub
//= require base