I'm right now implementing the new repository format into Arduboy Mate. Expect it to be available within the next few days.
With this new version you'll be able to use both, the old and the new repository format side by side.
It's already possible to flash local .hex, or .arduboy files. For example: You can download all the Team A.R.G games to your device storage and flash them using the file chooser in Arduboy Mate.
Yes it looks like it's not able to do USB-OTG. I'm very sorry