And another issue is that the current documentation tool (jsduck) can't follow the PureMVC define() hierarchy
I can't help you on this, I worked with JSDoc by the past, I also had many problem with it too and I've never worked with jsDuck. Tomorrow I've planned to start the work on PureMVC JavaScript standard framework. I also has to create help using jsDuck I hope I won't have any problem with it either.
Next to this work, I'll have a look into the full super implementation with PureMVC define().
