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But presumably the port touches the proprietary bits. So either A) that interface is not allowed to be distributed under the MIT license and they have a problem with Nintendo or B) the interface is fine to publish under MIT so why not make it more available?

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It's comparable to how open source code can also be patent-encumbered. It's MIT licensed but Nintendo's NDA still applies. The license can't supersede that.

I feel like the license definitely can supersede that - you obviously wouldn't be GPL compliant if you required everyone who got access to your code to sign an NDA, for example.

Nintendo's NDA would only apply to people that signed the NDA. If some third party acquired the code without signing the NDA, the NDA shouldn't apply to them.

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