So I thought I disabled Roots activation. I was wrong.
Activation still caused trouble, and digging deeper I eventually found a way to completely disable it. Ironically, the correct way that I eventually found was my initial gut instinct that I had before I made the fateful mistake of deleting the file instead of doing this correct thing.
And what is this “correct thing”? Just replace activation.php with a blank file. (That is, a file with a length of zero bytes if I’m not clear enough.) Yes really.
Astonishingly, even with activation completely disabled WordPress is still acting strange. Apparently it gets wonky if you are using more than one menu. Since I need eight to pull off this project, I’m sort of doomed to failure.
I’m going to resurrect activation.php to automatically reassign the menus. It’s ridiculous I have to do this but it looks like this is the only way out.