Hello, I recently gave a presentation at the lightning talk session at the ESRI 2015 DevSummit and a number of people had asked me to put my findings online and I figured that this would be a good place to share.
I found a way to get around using ArcGIS Online and Portal with the ArcGIS Web App Builder and use REST services hosted on your ArcGIS Server instead. It's a simple method that only requires that you edit the main config.json file and the MapManger.js file in the "jimu.js" folder. This workaround will enable you to develop a web map as you regularly would using the ArcGIS JavaScript API while using the Web App Builder to handle desktop and mobile
mtangtro/ArcGIS-Online-and-Portal-WAB-Workaround · GitHub
I still need to put proper instructions on the github page, but I hope to get that done soon.
Please ask if you have any questions!