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Hadrian: bring up to date with latest make improvements

John Ericson requested to merge wip/hadrian-clean-up-headers-logic into master

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.

Edited by John Ericson

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