upgrade iOS to phonegap 2.9
update android to phonegap 2.9
instead of using js to inject the correct cordova js file in to
index.html restructure things so that the common files are a level down
and the platofrm specific ones are directly placed in the relevant
project. This both makes for less fuss and also avoids the error with
Android < v3 instantiating cordova twice.

Note that the iOS common assets are included by a build script rather
than a symlink as symlinking doesn't seem to agree with Xcode