a way to link to files, like \verbatiminput, but NOT including the
contents of the file would be nice (for setup.py files).

a way to turn each mention of an API function into a link to its
documentation in the API reference would be *really* nice (this sounds
hard! parsing api.idx? brr!).

I surprise myself, but I think I'd like to see a javadocesque approach
to the API reference: associating each API function very closely with
its documentation in the source, and then maybe having a variety of
ways of arranging the results (e.g. by category (very high level
interface, abstract interface, concrete interface, ...) or
alphabetically).