Yeah, just relying on PATH seems to work, as long as one opens the correct dev prompt (the 64 bit one). But that's not very satisfying.
You can try the attached clang-win.jam, with using clang-win : : C:/llvm-6.0.1/bin/clang-cl.exe ; in user-config, or just using clang-win ; if clang-cl.exe is in your PATH. This shouldn't need a developer command prompt. It won't win any bjam toolset awards, but the old one didn't work and this does, at least for me, so there's that. Some libraries get confused when they see clang-win though, we have work to do. Thread, for instance, thinks that I want to use threadapi=pthread for some reason instead of threadapi=win32; Log fails with a link error: object_name.obj : error LNK2019: unresolved external symbol GetUserNameExW referenced in function "int `public: __cdecl boost::log::v2_mt_nt6::ipc::object_name::object_name(enum log::v2_mt_nt6::ipc::object_name::dtor$2::scope,char const *)'::`1'::dtor$2" (?dtor$2@?0???0object_name@ipc@v2_mt_nt6@log@boost@@QEAA@W4scope@01234@PEBD@Z@4HA) ..\..\bin.v2\libs\log\build\clang-win-6.0.1\debug\threadapi-win32\threading-multi\boost_log-clangw6-mt-d-x64-1_69.dll : fatal error LNK1120: 1 unresolved externals