My suggestion: a build system.
I like gulp, but grunt is well respected. You could even use Cordova hooks for the process I'm about to describe.
Essentially, you make your "www" directory a build artifact. Your real app is at "src", and your build process packages your files and then moves them into www. I've done it where the src file lives within the Cordova project and I've also done it where the src file lives outside the cordova project (essentially resulting in a "meta project"). I have reasons for preferring both, but I don't think it really matters. If using Cordova hooks, I'd probably keep src within the cordova project so you can use the cordova commands easily.
For example, my build process looks like this:
1) copy assets from src to www (files that don't need processing, like images)
2) compile scss to css and copy the result to www
3) package js files (using browserify), minify, and copy the result to www, replacing {{{VERSION}}} with the app version
4) copy config.xml from the meta project to the cordova project, replacing {{{VERSION}}} with the app version
My build process allows me to bump the version number whenever I want and a single build command ensures my cordova project (and thus my app) reflects that change. The build process can also execute specific Cordova commands, so "gulp build" can do the above copies, and then execute a cordova build, all with a single command.
Although I prefer gulp, grunt (and any other task runner) can do the same thing.
Now, that doesn't have anything specifically to do with Angular, but I would suggest that you should be able to build something similar for your project. If you do keep your src in your cordova project and use PhoneGap Build, be sure to add a .pgbomit file to the src directory so that PhoneGap build doesn't try to use it as the www.
Hope that helps!