The current phrase is
"including the user interface and persistence layers (such as JavaServer Faces (JSF) or JPA)"

and in the context of this particular wizard, we are focused on HTML5 & AngularJS. JSF is not applicable and is surprising to the reader/end-user.

I would say "including any web service and persistence layers (such as JAX-RS or JPA)" - I feel that is more accurate and more applicable to this AngularJS world.