(WIP) Loader - incorporate pathogen encoding logic in a separate module under loader.

This is a follow up to https://github.com/yui/yui3/pull/1813. 
I created this pull request specifically for feedback as to the direction that needs to be taken.

@caridy
@juandopazo
@ekashida
this also means the `core` collection has to be updated so it can attach the pathogen module as part of the initialization, we can talk more about this.