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This protects against… making many slightly-different copies of a malware app and signing them all locally, so that revoking one doesn't affect the others?

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This lets Apple nuke a compromised version of an app without doing it to all versions or apps by that developer. Which would have been useful in the case of Transmission [1][2].

[1] https://arstechnica.com/information-technology/2016/03/first...

[2] https://blog.malwarebytes.com/threat-analysis/2016/09/transm...

Transmission’s Developer ID cert wasn’t compromised, the compromised binary was signed by a different developer.

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