Re: Design flaw?
That would be fine, except..."
I don't see that. When you create a GitHub account you sign up to its Terms and Conditions. They can be amended to set out the revised withdrawal process, specifically that material will remain for say a week or a month before being purged. Posting of copyrighted material constitutes release of the material under said terms. Any file altered under the new terms will constitute acceptance of them for the whole file. A little bit of coding to implement different algorithms for files with different datestamps, and bingo! Job's a good 'un.
If a third party is demanding takedown, there must always be a reasonable time period for this to be implemented. Just make sure that the GitHub delay squeaks within such a reasonable period.