While copying Sencha Touch 2 files to Cordova i use the following command to create a production build;
sencha app build production ../App/MyAppProj/www/
When i execute this command, all the files in ST2 project gets added to the WWW directory, and not the folders and the files containing in those folders.
How should i add these files which are in sub folders in the ST2 application
Once you build your application using the SDK, you will no longer need your app folder. The SDK will generate a minified (or non-minifed) js file containing all your views, controllers, stores and models that you have created in the app folder.
I suggest you read the documentation about Builds. Once you have your app ready for deployment, you need to modify your HTML file to point to sencha-touch.js. During development you will usually point to sencha-touch-debug.js.
Once you build your app using the SDK. You will have the production version of the sencha touch library and your app.js (or whatever you name it) in your HTML. There will be no need of app folder, src folders etc in production environment.