BackboneJs + RequireJs AMD multi-page boilerplate.
github.com
github.com
https://github.com/documentcloud/underscore/pull/431#issueco...
In the meantime, as long as you are using the right "shims" you should be able to work fine with the stock copy of Backbone. (It looks like a correct "shim" defines the load order and returns a backbone object, not a closure (I am looking at app.js and am 50% sure that it is a closure, but I could be wrong))
From digging through the above link, it looks like the removal had something to do with how the libraries were being loaded in.