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Perhaps I'm misunderstanding the system. Looking through it now it seems you're actually handing off to WordPress to update the files, and providing information for it using the genesis_update_push function? If so then WordPress would respect the constant and not attempt to update?
If so, then really I'd just recommend hiding the option panel if DISALLOW_FILE_MODS is set to true, as the options are no longer used anywhere.
Excuse me, I linked to the wrong constant, you're correct about DISALLOW_FILE_EDIT, I was thinking about DISALLOW_FILE_MODS; my mistake. I use these constants because we manage WordPress sites with git and composer, composer managing plugin and theme dependencies (such as Genesis). Allowing WordPress or Genesis to autoupdate makes the production, development, and staging go out of sync; which can cause issues during development.
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