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There is no black box involved in the process. The Signal app is open source. The whole point of the app is providing end-to-end encryption from client to client. You seem to be confusing end-to-end encryption with transport encryption. It doesn't mean what you seem to think.
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It uses authenticated encryption with forward secrecy between instances of the app. It doesn't trust the server. Encrypting connections to the server is not end-to-end encryption. End-to-end means encrypting from one end (Signal app) to the other (Signal app), not to the server.
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You have to do something wrong for Android apps to not have reproducible builds because the SDK and Android gradle plugin makes them reproducible by default. It defaults to using a placeholder for timestamps, etc. such as the timestamps in the zip. Not really much work for devs.
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