You're not allowed to circumvent for format shifting, but you are allowed to circumvent to access a work you have rights to. So these takedowns on GitHub should not be happening.
You are allowed to circumvent to access a work. No one is allowed to publish a method to do so (well, I believe the original copyright owner might be?).
So, most likely this GitHub takedown is perfectly legal.
The law allows people to circumvent copy protection to access works they are entitled to access. There is also a provision against sharing copy protection breaking methods.
I never interpreted them as clashing, merely that I can't knowingly share copy breaking mechanisms with people who are unauthorized to use a work. If they do clash then you have to side with the consumer.
> The law allows people to circumvent copy protection to access works they are entitled to access.
Claiming that such an allowance exists is not the same as actually identifying the statute or ruling that creates the allowance. What is your textual basis for claiming that there's a general permission for circumvention?
> If they do clash then you have to side with the consumer.
This sounds like you're referring to a concept that exists in contract law, but has no applicability to a question of how to handle a conflict between two provisions in law. In such a case, the courts will usually uphold whichever provision actually exists in the text of the law.
Have you actually read the law you're discussing? It was in the first amendment to the DMCA, because they realized they can't prevent people from accessing things they paid for.
I can't actually find the thing I am looking for. AFAIR the Cornell law site does not have the updated version that I need to reference, but you can see by the exemptions granted they are just codifying your rights to continue to use a work, even if it is not necessarily obsolete, if the copy protection has gotten in your way.
To actually change this rightsholders would have to lease works instead of selling them, but they still use the word "sell" when interacting with consumers.
So, most likely this GitHub takedown is perfectly legal.