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).

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Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2461/do-not-include-cctkh-file-in-flesh