Thanks for your kind words about our product. We are also very excited about it.
Now onto your questions. The reason why we need the files on the device's storage is to enable the LiveSync
support. As you have noted those files will be there only when you are building and debugging the application. We are currently working on "Publish to App store /Marketplace" functionality that will produce release builds ready for submissions. In those release bits the files will be bundled in the apk file.
Regarding your other request about minifying/uglifying scripts files it is something we have been discussing internally in the team for some time now. It is definitely in our backlog, so stay tuned.
Have a great day.