One of our Google Apps scripts sometimes fails to push to Github, with the error message "(filename) does not match " - the quick fix is to just delete the relevant file(s) (filename) in the git repo, and run the script from the console - it would then successfully push, and retain the correct hash for the next push.
Edit: link to a repo with example GAS code for pushing a file to a github repo - a json file to a github pages site in this case - https://github.com/hn-88/GAS-daily-upload-to-sched
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