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Or alternatively, the developer/maintainer or whoever does the bundling can simply use some sort of cryptographic key, which the installer uses to confirm the new bundle is indeed from the same source as the already installed bundle.

Basically, the problem you're trying to solve is intrinsic to any form of installation, not only the idea posted in this article, so whatever solutions exist already can be used without any need for centralised administration.

If I recall correctly, zero-install used some crypto-signing for something similar.

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