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
The cordova js the only js file needed. This is autogenerated when you ran the phonegap create script.
index.js contains sample code on how to bind to the deviceready event. It can serve as a start for your js code.
The spec folder and spec.html are for javascript testing using Jasmine, a BDD testing framework for Javascript.