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To my mind, the actual problem is neither one of those things, but if Github is wrapped up into some new project. Many of the citations for Github aren't for software, but as a stable, open store for data.

Which means if that URL changes, that link - in a physical paper - goes stale.

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If you need stable links then buy yourself a domain or use a URL shortener that you can update. Might be wise to also provide content hashes of the data you're referencing in your paper.

Even if it does get merged or renamed, I don't see why Microsoft wouldn't forward the URLs.

Link rot is a real issue in general though, I don't mean to minimize that.

I agree - which is why I haven't moved my lab's accounts.

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