Cleanup .entries vs. .options.entries in bundle config

[stephanwlee]

In bundle object, we current have
config.entries vs. config.options.entries which mean totally two different things:

• former: describes modules associated with a bundle
• latter: describe entry or entrance to an application (entry in browserify sense; we will execute this module as we bootstrap)

Those two are extremely confusing and we have to clean this up (generators and outlets will need to change appropriately).