I was using Git wrong. This is why many of Pjotr's messages have been confusing to me, and no doubt many of mine have been for him. This is all supposed to be done in a branch of biolib, not in its own tree altogether.
Of course, now that I've done things right, I can't figure out how to push back up. Somewhere, Git is just crashing out. Looking for help online seemed to indicate that there's a mismatch between the version I pulled, and what I'm trying to push. But nope--repulling doesn't help.
Meanwhile, I did manage to recreate my .i files. And guess what? SWIG still claims there's a syntax error, right on the same line.
Bleah. New day tomorrow.