There's something weird going on with cmdoption... I've applied for subscription to the docs mailing list, but while I'm awaiting moderator approval, here's the brain-dump. Suppose this option description:

.. program:: trace

.. cmdoption:: -c, --count

   Blah blah blah

And now this reference:

This is a test long :option:`--count` and then short :option:`-c`, test.

Only the -c gets linked to ..cmdoption, not --count.
If I list --count before -c in ..cmdoption, then it's the other way around. What makes it kinda work (link both the long and short names) is:

.. cmdoption:: -c
               --count

   Blah blah blah

But this isn't standard (although it doesn't look too bad). Actually, the original listing (the short name first, then the long one) is customary in the library docs.