In my hosted app published at: http://mobile.nevadaopera.org/Opera.html the behavior is a I described in the steps above. The links open in the same window. The only way to return to the app is push the home button and re-open the app from the home screen. This is on iOS 6. I'm going to try an hack ...
I've developed an app and when testing on iOS I found that opening a HTML5 Web App from the Home Screen (using the Add to Home Screen option from the browser) handles opening hyperlinks differently than from within the Safari Web browser. Steps to reproduce: Create a publish a HTML5 Mobile Web App w...