Updates the handling of the create machine callback handlers to update the existing model instead of destroying and re-creating

Destroying and re-creating the machine model caused the tokens to disappear then re-appear when the deltas came in. Updating the models instead keeps them in the DOM.

Created a new module called 'yui-patches' as a place to put monkey patches to the YUI codebase.
I expect that we will convert everywhere which is currently doing it's own parsing to call this method with the model in the future to determine if its committed. That's out of scope for this branch.