I think I have Git under control. I have my own branch (biopp) inside of my own fork, and I'm successfully compiling things with very little effort. Pushing and pulling all seems to work, as do Pjotr's CMake macros.
The downside--tried using SWIG on more .i files: this time from NumCalc. (Aside: it occurred to me that I don't necessarily need to actually SWIGize Utils, since no one calls it directly, anyway.) The result was exactly the same. Something's not working, somewhere, and I still don't know why. I've sent queries to both the CMake and SWIG mailing lists, but so far no one's replied. Gotta keep plugging, and hope the answer presents itself soon.