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Publishing an application in MonoDevelop and Visual Studio results in different .apks.
I unzipped the apk files and noticed that the .RSA and .SF files are different between the two apk's. The apk published from MD has names similar to my keystore, but the apk from VS has named the two files ANDROIDD.RSA and ANDROIDD.SF. It looks like Visual Studio is not using the keystore names/keys.
This issue is that Visual Studio was trying to re-sign and already signed package, the signing tool was ignoring the new keys and using the old ones.
Fixed in master/44eae0a9e4