So today I totally broke this site. I removed the Ubuntu supplied version of Nikola 5 from the machine I am using to write on this blog and installed Nikola 6 from sources. I then, stupidly, built and deployed the site to the webserver using the newly installed Nikola 6.
Only after refreshing my browser I noticed that I had totally broken my custom theme and I had no way of recreating it, because I had stupidly not made a backup of the custom theme. I subsequently found the base theme I am using, Slate from Bootswatch, will not work correctly with Nikola 6 generated HTML. So I am using the default, Nikola supplied, Bootstrap theme for the time being.
I have fixed the Typekit integration, so the fonts are back to their original goodness.
Work in progress, as they say.