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As we all know, MANIFEST.MF contains sha1-digest encoded in base64 for all the files in apk, CERT.SF contains sha1-digest of file MANIFEST.MF and all items in it, and CERT.RSA contains signature for file CERT.SF and a certification.

Here is the question: Why not just sign MANIFEST.MF and save the signature in CERT.RSA directly?

expoter
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The apk protection chain is .(RSA|DSA|EC) -> .SF -> MANIFEST.MF -> contents of each integrity-protected JAR entry.

As per official android page [website][1]

.SF file contains a whole-file digest of the META-INF/MANIFEST.MF and digests of each section of META-INF/MANIFEST.MF. The whole-file digest of the MANIFEST.MF is verified. If that fails, the digest of each MANIFEST.MF section is verified instead.

Thus, CERT.SF is added to provide fallback mechanism for signature verification.

user3560691
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    could you please elaborate more about the "fallback mechanism" here. Why it happens? – Long Sep 15 '19 at 10:35