@trn579s,
Mobione merge only screens that are referenced by a go to Screen action. In this last Wayne’s example the goal is navigate beetween screen when the item on combobox is changed. So, it was necesary use the link hack, creating a design(screen-links) with a link to screen1 and screen2, and on main design you have a other link referencing to this last design(screen-links).
But now you can avoid this hack using Additional Project Files property, you just need add screen1.mobi and screen2.mobi and example will work in the same way.
For .js files you should use Javascript Libraries property, 3rd party js files go to www folder as is.