In Thym, the app.initalize() is called in a script tag inside the index.html but in a cordova CLI generated project (cordova create) , the app.initialize() is called directly in the index.js .
I think Thym should align with this.

To verify:
1. Create a new project and observe that index.html does not call app.initialize() in index.html but rather on index.js
2. check that project runs on CordovaSim