Turns out the problem was keyboxd was waiting for a lock. Unfortunately I wasn't able to find the lock: so, after making a backup, I decided to resort to harsh measures: I nuked my .gnupg directory. Now GnuPG is getting a little further along, but it's still not working properly.

Let's start by nuking the .gnupg directory and shutting down all GnuPG daemons:

rjh@ripley:~$ rm -rf .gnupg
rjh@ripley:~$ /usr/local/bin/gpgconf --kill all
rjh@ripley:~$ ps ax|grep [g]pg-agent

No output: gpg-agent is gone, and I'm assuming other GnuPG daemons are, too. Next, verify we have a /usr/local/bin/gpg-agent and that it points to the correct GnuPG helper programs:

rjh@ripley:~$ ls -lh /usr/local/bin/gpg-agent
-rwxr-xr-x 1 root root 2.3M Dec  5 20:19 /usr/local/bin/gpg-agent
rjh@ripley:~$ /usr/local/bin/gpgconf --check-programs
gpg:OpenPGP:/usr/local/bin/gpg:1:1:
gpgsm:S/MIME:/usr/local/bin/gpgsm:1:1:
keyboxd:Public Keys:/usr/local/libexec/keyboxd:1:1:
gpg-agent:Private Keys:/usr/local/bin/gpg-agent:1:1:
scdaemon:Smartcards:/usr/local/libexec/scdaemon:1:1:
dirmngr:Network:/usr/local/bin/dirmngr:1:1:
pinentry:Passphrase Entry:/usr/local/bin/pinentry:1:1:

All looks good.  Let's launch gpg-agent.

rjh@ripley:~$ /usr/local/bin/gpgconf --launch gpg-agent
rjh@ripley:~$ ps ax|grep [g]pg-agent
 229366 ?        SLs    0:00 /usr/bin/gpg-agent --supervised

Wait, what? Why was /usr/bin/gpg-agent (system-provided, version 2.2) used instead of 2.3?

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