Hadrian: bring up to date with latest make improvements

Headers should be associated with the RTS, and subject to less hacks.

The most subtle issue was that the package-grained dependencies on generated files were being needed before calculating Haskell deps, but not before calculating C/C++ deps.

The other tricky thing is the hoops needed for genapply's weirdness, but that is at least easier to document in the code, as has been done.