cctk.h contain partially auto-generated content that is not always sensible for the flesh, eg CCTK_THORNSTRING is "src"
Removing these files has the nice side effect (and reason I tracked them down) that after a:
make sim-cleandeps rm configs/sim/config-data/make.thornlist
one can copy the compiled Cactus tree to another location (or tar up and offer in a tutorial server) and a latter
make sim will only compile a very few files (namely a file that contains the name of the Cactus main directory).