Wow, that's awesome to hear! I have a Mindstorms NXT 2.0 brick, which iOS devices cannot communicate with directly (because it supports neither Bluetooth LE nor wi-fi). Nice to see that things like these are now possible with the new EV3 brick.
Stash has the git command built-in, so you should be able to work with your Git repo directly from there. If you haven't already, you should make a folder for your repo, cd there and then run git clone https://github.com/yourusername/yourreponame.git. Now you can make modifications to the files locally. To push the changes back to GitHub, first run git add on any changed files, then git commit, then git push. (The first time you commit and push, you'll be asked to enter your GitHub e-mail address and password.) If you push any changes to the repo from your PC, you should run git pull in Pythonista to get the changes there too. On your PC you should hopefully have the GitHub Desktop application installed, which makes the whole process much easier for Git noobs like myself. ;)
As for the brick, IMO you shouldn't use it as permanent storage for anything. The NXT 2.0 had very limited storage and you couldn't do any serious programming on the brick alone, so keeping any files on there permanently wasn't really an option. The way I worked with it was basically "write it on the PC, compile, upload to NXT and overwrite anything else that was there". Not sure if this has changed in any way with the EV3, or if your workflow is different, but that's how I do it.