What I have found so far is that it groups everything alphabetically when adding scripts. So if I add a base class after I add the super class, it fails because the base didn't load. If I then create a sub folder called "A" and move the base class into that folder, it's not read before the super class and everything loads.
Not sure if they'll give us more flexibility with this later on, but you can make it work.
I have almost reworked my entire game into mostly JavaScript and that's how I worked around it.