Mario pointed me to this bug, and i'm surprised that this happened.  I
also am not sure how to debug it because it's not something i've been
able to reproduce myself, and it sounds like once it's fixed for
someone, they have no incentive to go back and reproduce it themselves.

Can anyone provide a set of reproducible steps to make this happen?

For example, as a standard user, i can do:

 gpg --gen-key

and then the new key is visible via both "gpg --list-keys" and "gpg
--list-secret-keys"

if i then do:

 gpg2 --list-keys

i can also see the new key.  and if i do:

 gpg2 --list-secret-keys

then i see:

gpg: starting migration from earlier GnuPG versions
gpg: porting secret keys from '/home/testuser/.gnupg/secring.gpg' to gpg-agent
gpg: key 57B78432: secret key imported
gpg: migration succeeded

and subsequent attempts to use the gpg2 secret key work just fine.

do you have any keys on smartcards, any keys ancient or weirdly-
formatted keys, or any other unusual configuration that might have
triggered this problem?

without a way to reproduce the error, i'm kind of at a loss.

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https://bugs.launchpad.net/bugs/1565963

Title:
  gpg secret keys not migrated after upgrade to gnupg 2.1

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