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If the developer provides a self-updating mechanism for their app, it makes a lot of sense to get it directly from them. F-Droid has serious issues with the security of their infrastructure and the app. Updates are often very delayed and they make undocumented changes to apps.
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If GitHub was compromised, the code obtained by F-Droid could be modified by an attacker too. Android pins signing key and version for apps after the initial install, so the developer would need their key compromised after the initial install or it would be detected as invalid.
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