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Incorrect app id reuse leads to users reporting the same key pinning errors upstream over and over. F-Droid also places a substantial burden on upstream developers by distributing their own builds of apps with undocumented downstream changes and significantly delayed updates...
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The app id reuse also causes significant usability issues beyond the key pinning errors users encounter across profiles. Users run into similar issues with updates. F-Droid will think it can provide updates to an app installed from elsewhere and vice versa for Play Store, etc.
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Some developers create these issues on their own by not using separate app ids for different variants of their apps, but many are handling this properly and most don't have incompatible variants available. F-Droid is the elephant in the room making this a common real world issue.
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