Ikiwiki has been, for a time, throwing an error on pushing to the repo or setting up or forcibly calling the update script. The exact error was:

Can't call method "merge_influences" on an undefined value at /usr/share/perl5/IkiWiki.pm line 2072.

The solution was to completely and utterly remove ikiwiki, then to re-install it. I also had to correct permissions in my public_html where the wiki was stored, as several of them had been set to root:root (I'm sure by some of my thrashing about). After they were all correct permissions, and ikiwiki was re-installed, calling ikiwiki -setup .ikiwiki/shades.setup correctly generated the wiki at my webspace. Yay!