I, for one, handle it with a tool that mimics the compiler's preprocessing phase and emits both redo-ifchange information for all of the headers that are used, and redo-ifcreate information for all of the non-existent headers that are looked for during the process.

    JdeBP %cat test.cpp
    #include <cstddef>
    void f() {}
    JdeBP %/package/prog/cc/command/cpp test.cpp --iapplication . --icompiler-high /usr/local/lib/gcc5/include/c++ --icompiler-low /usr/local/lib/gcc5/include/c++/x86_64-portbld-freebsd10.3 --iplatform /usr/local/include --iplatform /usr/include  -MD -MF /dev/stderr 2>&1 > /dev/null|fgrep redo
    redo-ifcreate ./cstddef ./bits/c++config.h /usr/local/lib/gcc5/include/c++/bits/c++config.h /usr/local/include/bits/c++config.h /usr/include/bits/c++config.h ./bits/os_defines.h /usr/local/lib/gcc5/include/c++/bits/os_defines.h /usr/local/include/bits/os_defines.h /usr/include/bits/os_defines.h ./bits/cpu_defines.h /usr/local/lib/gcc5/include/c++/bits/cpu_defines.h /usr/local/include/bits/cpu_defines.h /usr/include/bits/cpu_defines.h ./stddef.h /usr/local/lib/gcc5/include/c++/stddef.h /usr/local/include/stddef.h ./sys/cdefs.h /usr/local/lib/gcc5/include/c++/sys/cdefs.h /usr/local/include/sys/cdefs.h ./sys/_null.h /usr/local/lib/gcc5/include/c++/sys/_null.h /usr/local/include/sys/_null.h ./sys/_types.h /usr/local/lib/gcc5/include/c++/sys/_types.h /usr/local/include/sys/_types.h ./machine/_types.h /usr/local/lib/gcc5/include/c++/machine/_types.h /usr/local/include/machine/_types.h ./x86/_types.h /usr/local/lib/gcc5/include/c++/x86/_types.h /usr/local/include/x86/_types.h
    redo-ifchange /usr/local/lib/gcc5/include/c++/cstddef /usr/local/lib/gcc5/include/c++/x86_64-portbld-freebsd10.3/bits/c++config.h /usr/local/lib/gcc5/include/c++/x86_64-portbld-freebsd10.3/bits/os_defines.h /usr/local/lib/gcc5/include/c++/x86_64-portbld-freebsd10.3/bits/cpu_defines.h /usr/include/stddef.h /usr/include/sys/cdefs.h /usr/include/sys/_null.h /usr/include/sys/_types.h /usr/include/machine/_types.h /usr/include/x86/_types.h
    JdeBP %/package/prog/cc/command/cpp test.cpp --iapplication . --icompiler-high /usr/local/lib/gcc5/include/c++ --icompiler-low /usr/local/lib/gcc5/include/c++/x86_64-portbld-freebsd10.3 --iplatform /usr/local/include --iplatform /usr/include  -MMD -MF /dev/stderr 2>&1 > /dev/null|fgrep redo
    redo-ifcreate ./cstddef ./bits/c++config.h ./bits/os_defines.h ./bits/cpu_defines.h ./stddef.h ./sys/cdefs.h ./sys/_null.h ./sys/_types.h ./machine/_types.h ./x86/_types.h
    redo-ifchange
    JdeBP %

I also have a wrapper that takes arguments in the forms that one would invoke g++ -E and clang++ -E, tries to works out all of the platform and compiler include paths, and invokes this tool with them.

It's then a simple matter of invoking these redo-ifchange and redo-ifcreate commands from within the redo script that is invoking the compiler.

You can see this plumbed into redo in a real system in the source archives for the nosh toolset and djbwares.

* http://jdebp.eu./FGA/introduction-to-redo.html#CompilerDefic...

* https://news.ycombinator.com/item?id=15044438