I also find it strange that the deploy route is affected by the appFolder. Why should a deploy behaviour be changed by a project configuration? Well this is to general... An example for a potential problem:
Am I missing something? Thanks for your help and a great project. love it so far!
well your double entering it in this case. Simply make your deploy path /webapp/
The limitation is that by convention MVC requires an app folder that has models/ views/ controllers/ etc .. underneath it.
Know that in the future we'll be evolving the deploy to do move than rsync / xcopy files. Think "sencha app build production" aka better integration with SDKTools to deploy your application for production
Sencha Architect Development Team