Renamed App* AutoBeans to PipelineApp*.

To help avoid name conflicts with the App class in this repo and in the org.iplantc.core.uiapplications.client.models.autobeans package.
Refactored serialization methods to use AutoBeans.

Added Pipeline AutoBean serialization methods to PipelineCreator and DragCreator, and Input/Output AutoBean accessors to App.
Deprecated the JSONObject versions of these methods.