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First, the secret key packet as such doesn't have a version number.
There is no deep reason that it couldn't. Instead of forcing a
tight coupling between the two, give it its own version byte
(starting with 5). The whole public key packet (or just its contents)
could follow, including its (independent) version number.
Another place we could represent the alternative format is the byte
which comes shortly before the S2K in the secret key packet.
A fine alternative... keeps the compatibility hacks together. How
about 254?
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=kjmv
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