Add tests for pathogen encoder.
Add `extendedCore` config to yui for adding `loader-pathogen-encoder`.
Add `comboHander` config to yui for allowing the use of pathogen encoding logic.
Update loader to use pathogen encoding logic when `comboHandler` config is set.
Add `loader-pathogen-encoder` submodule.
Update build and meta files for `loader-pathogen-encoder` submodule.

 Changes to be committed:
	modified:   loader/build.json
	modified:   loader/js/loader.js
	modified:   loader/meta/loader.json
	modified:   yui/js/yui.js
Undo change made to yui for testing.
Code style changes.
Use boolean for determining whether modules need encoding.
Fix issue in which sorting broke in phantomjs and versions of android.
Replace JSON.stringify with Y.dump for logging.
Remove NAMESPACE for customComboBase. This will be passed as part of the config now.
Test to ensure loader falls back to default combo if no customComboBase exists.
Loader should fall back to default combo when no customComboBase config has been specified.
Added assert true to optional dependencies and patterns test to prevent failure in phantomjs.
Merge branch 'dev-master' into combohandler
Build files for loader update.
Merge branch 'dev-master' into dev-3.x

Conflicts:
	build/yui-base/yui-base-coverage.js
	build/yui-base/yui-base-min.js
	build/yui-core/yui-core-coverage.js
	build/yui-core/yui-core-min.js
	build/yui-nodejs/yui-nodejs-coverage.js
	build/yui-nodejs/yui-nodejs-min.js
	build/yui/yui-coverage.js
	build/yui/yui-min.js