I just downloaded arduino 1.0.6, pulled everything from github, added the sdfat library, opened mainArduino in arduino, and hit compile. If you use a usbAsp cable, you can upload it using that straight from arduino.
If you want to use the updater and a USB cable, not sure if it works on 2.3HW it doesn’t on 2.1, you can find the temporary hex file it creates and move it to the correct location, and update away. If you are having trouble finding the hex file, turn on verbose mode for “verify” and one of the last lines will have the file name and location.