Alright, I am just getting started with phoneGap for iOS and I am noticing in the www directory that there are plenty of files, such as
spec/helper.js
spec/i
spec/helper.js spec/index.js jasmine
You do need these files, if you want to keep your app in Behaviour Driven Development. These are basically for unit testing.
Cordova.js/Phonegap.js are the scripts that make your application "Phonegapifiable". Adds that extra something on your webapp so that it can be deployed as an app.