You have 2 requirements here:
- Managing a common code base across applications
- Branding and distribution
So to lay the ground work what I would do is create a base project, which includes all of your cordova plugins, config and assets which will be required by all your customers.
The angularJS application should be a module that you can put in a
lib folder outside of
www and manage it as a gitsubmodule, this will allow you to update your codebase across all your customers without having to copy paste code.
Then all you need to do is create a config file which is specific to that customer - assets, labels, translations etc that your lib application looks for and uses to pull in the customer config.
You could make this as part of your gulp tasks when building the application.
Managing your resources and
ionic.project and app id will be restricted to a single project. But if you follow the structure above you can clone the project for as many customers as you require, maintain a single code base and write additional code if required without it affecting your common library application.