All code to be conditional on setting of epubversion. This is a stylesheet parameter that can be set using epubversion=3.0.1 or epubversion=3.1 on the saxon command-line.
Update version number of generated ePub. [DONE]
Remove use of the the refines attribute. [DONE]
Remove the OPF2 meta element.
Remove the NCX [Not yet needed]
Remove the guide element
Remove the binding element [Never used, but verify]
Adjust output CSS files, now that restrictions are lifted.
ePub 3.1 is out since January 2017. For details see http://www.idpf.org/epub/31/spec/epub-spec.html, and in particular http://www.idpf.org/epub/31/spec/epub-changes.html.
For now, intent is to put this behind a setting.