I am having the same issues. My apps are getting cached for the users and in order for them to get a different version I create a redirect from the root folder to a new folder..
I have tried modifying the index page and it did not help as I expected. I also added the necessary meta tags in the index page with no result...
I think ESRI should have an option to use the dojo preventCache parameter in all the widget file requests.
If anyone knows of a way to force the app to do this I would be interested in seeing the implementation.
As of now I am digging around the the WidgetManager.js file to see if I can append my own unique ID onto the end of each URL request. Its a little dirty as I would prefer to not modify the core code of the WAB.
Drew