Hi Jem,
In 1.0.1 update we re-worked app creation options. By default, an application is initialized with the following options enabled:
‘Player-Based’, ‘Create Starter Files’ and ‘Use Puzzles’.
This means, that the stock player will be copied into your app folder and renamed. This way it won’t be using stock player files anymore. So you can freely modify the copied JavaScript file, adding any new functionality.
On the contrary, the ‘Custom’ generates a very basic set of files (no Puzzles for example). This option is more close to the original Three.js approach and should be considered for creating pure JavaScript-coded applications.
I’d recommend to stick to the ‘Player-Based’ option since it can be conveniently used by programmers and designers at the same time.