The latest sys-devel/clang ebuild (2.9) has some changes, which should, from my point of view, be incorporated to the trunk ebuild. I am using clang trunk and especially had problems, because --with-c-include-dirs=/usr/include:${CXX_PATH}/include" is missing in the trunk ebuild. Reproducible: Always
Created attachment 274891 [details, diff] proposed patch clang-2.9-darwin-prefix.patch does not apply cleanly on current trunk, so I did not merge it. And I don't understand the change inside src_install() -> if [[ ${CHOST} == *-darwin* ]] so I did not merge it, either.
Thanks for spotting this! Indeed clang (and also llvm) live ebuilds lack some of the recent changes. I'll fix them ASAP
llvm-9999 and clang-9999 are now up-to-date again, thanks for the report and patch!