`rts` and `ghc-prim` now no longer have a `*.cabal.in` to set Cabal flag
defaults; instead manual choices are passed to configure in the usual
way.

The old way was fundamentally broken, because it meant we were baking
these Cabal files for a specific stage. Now we only do stage-agnostic
@...@ substitution in cabal files (the GHC version), and so all
stage-specific configuration is properly confined to `_build` and the
right stage dir.

Also `include-ghc-prim` is a flag that no longer exists for `ghc-prim`
(it was removed in 835d8ddb) so I got
rid of it.

Co-Authored-By: Matthew Pickering <matthewtpickering@gmail.com>