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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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That's where F-Droid is obtaining the code to build after all. They're an additional trusted party and known to have poorly updated, insecure infrastructure and security practices. You don't avoid trusting the developers or their security by getting it through F-Droid.
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