I had messed up them, completely deleting the theme's functions.php file. This should fix #22.
The 'hybrid' theme structure has changed and the file that was being patched no longer exists.
not all of them apply cleaninly (sorry). See #15 and #5 for the list of things to fix.
the plugin has been abandoned, I have moved it to ai-mu-plugins for the moment. Closes #17