Refinement for CompilerManager include paths

Hi Anders,

I'd like to push my latest CompilerManager code tweaks along with some other small fixups. Commit 6000b2b has the primary details. The earlier commits are left over from the last pull request that you manually merged.

This code, I believe, does a much better job setting the proper std and implicit include paths, at least under the work I've used it with clang and MacOS. 

Let me know if you have any questions.
Joe