I don't see reference to cordova.js
in your source and it's the only cordova-specific file you need to add. Using Cordova 3 CLI the plugins are imported automagically by scripts in cordova.js (no need to add reference to plugin's JS file).
Edit.: BTW don't copy the cordova.js file to your app folders, just use <script src="cordova.js"></script>
in your html. The file specific to given platform will be placed in the platform's www
folder during cordova prepare
.