From what I understand, you just want to develop mobile friendly websites and to get android apps out of them, right?
For this, app.js (used in DroidScript) will give you access to standard UI composant, popup messages, custom alerts and confirm dialogs, etc.
If you don't use them, you basically don't need app.js.
DroidScript can effectively provides you its IDE, and you can use its (paid) apk plugin to generate your applications.
Just create a "New HTML App" from DroidScript IDE and it will generate your "index.html" file (which will have the name of your project).
Place your code, and there you go :)
Do you need any specific functionality?