I am finding more useful resources for AngularJS, including Christopher Hiller's Developing an AngularJS Edge (Bleeding Edge). What I am going to do here is describe the structure I have come to after a lot of refactoring in my Rhizome application, using AngularJS and Saxon-CE. It's not perfect, but I do want to document it at this point. I'm using PhoneGap, so this all resides in assets/www:
lib/rhizome/css - contains rhizome.css, references to Gaia css
lib/rhizome/js - contains Controllers.js, PresentationServices.js
res/views/html - contains pmixRequest.html, pmixResponse.html
res/views/xslt - contains PMPPrescriptionReport-application.xslt, other stylesheets
The stylesheets still need some work - I started out building a pure Gaia application for Firefox OS, before porting into PhoneGap for Android, but I have retained some of the Gaia look and feel. I am also considering leveraging AngularUI/Bootstrap for this purpose.
All of my controllers are in a single file, and align nicely with my views. The Presentation Services contains my rendering service and Business Services is currently empty. I am sure I will require some business logic eventually. My main AngularJS module is declared in a script tag near the bottom of my index.html page, and called at the top in the html element.
As far as my views are concerned, I have a pair of partial HTML forms which align with the PMIX Request and Response interactions, and a separate include file for the header, to reduce clutter. I may actually rename the controllers PMIXRequestCtrl and PMIXResponseCtrl, to make it obvious that is what they are. I'm used to HL7, where interactions have well-defined interactions. I like the alignment between controller and partial HTML view.
For the Saxon-CE piece, I have a separate set of template views. I'm not as happy with these, but they serve a purpose. In the long run, both the HTML and XSLT views should be largely generated from the PMIX CAM schema. I have put these in the res directory because they are resources.
My approach is resource-based, whereas the PMIX data is really not. Three resources are represented in the PMIX payload: Patient, Prescription Report and Prescription. These are clipped out of the response message and then bound to the model scope in pmixResponse.html. This would be cleaner and more RESTful if the PMIX schema was broken into more granular interactions, but that's okay.