I decided to test flashing the Gemma before sitting down with Silly Goose Monkey (SGM). I am so glad I did since it did not go smoothly. Following the instructions at Adafruit, it turns out the programmer on the Gemma has known issues with USB3.0. I ended up having to order a USB 2.0 hub to provide protocol translation. After I tried flashing through the hub, I was able to quickly flash the Gemma with the test sketch.