I was trying to update the "whole index" tests, but found the nav doc was integrated into the content. When I split it out per the minimal epub, I started getting this error:

nav.xhtml(2,110): Error while parsing file: At least one 'index' element must be present in a document declared as an index in the OPF.

I don't see why a nav doc (esp. not in the spine) would be expected to have an index, though. I can't find anything in the indexes spec that would corroborate this error, so I'm assuming it's epubcheck being overzealous.

For now, I'm just going to add the extra expected error and give preference to the common file structuring.