Same issue. It seems that encrypting the files will cause the main.js to be impossible to locate. It's a pity if we can't use encryption and source code protection.
There's one thing I forgot to mention: in my game, the "generator" folder is handled a bit specially; due to plugin compatibility, I've moved it to be placed directly under another folder.
It's possible. It would usually be that a file is missing (if it was now stored on the root folder of the project and wasn't added to the custom files and folders list).
