doc: use program and option directives to document options

Use the program and option directives to document the subcommand
options. This unifies a lot of option documentation throughout.

This also makes it possible to reference options with :option:`--foo`
(within .. program::) or :option:`subcommand --foo` (globally). This
is left for later work.

See https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html#directive-program

Note: There is a lot of indentation change, but intentionally there is
no reflow. Using 'git diff -w' or 'git show -w' to ignore white space
changes makes this a very easy change to review.