Nice changes! Especially the program/cmdoption directives combo.

Your patch introduces trailing whitespace (good editor settings can show those, as well as hg diff with the color extension) and has one unnecessary change:

-line, ``options.filename`` will be ``"outfile"`` and ``options.verbose`` will be
+line, ``options.filename`` will be ``outfile`` and ``options.verbose`` will be

In this case, the things in ```` are not command line snippets but Python code, so the quotes are regular string notation.

Attached patch fixes that.