MPI affinity: enable, but behave better if not enabled

examples/Makefile.am sets affinity for MPI runs if we can, but examples/main.c doesn't pin the main thread if engine_init won't be pinning the runners. I've checked with top that this means we use multiple cores in both cases, vs. the current scenario of everything ending up on one.

Also restore the getopt -o option lost in a merge, I think.