The issue seems to be how I structured my project. When SDF was released I started adding projects to my main project/workspace folder as new customizations came up, and I can open those SDF project folders fine in WebStorm and have all the NetSuite functionality. The loss of the NetSuite context menu in WebStorm seem to come from me opening the root project folder. In Eclipse I could open that root folder, containing SDF project folder(s) and one non SDF project folder. I still had the context menu on the non-SDF folder as well as the SDF folders. In the non-SDF folder I was just deploying via the upload keyboard shortcut