To use the new libc++ you *should* manually tell clang to pick it up. Fiddling with `lib/c++/include` and `lib/c++/v1` *can* lead to trouble. I don't think it does in this case because apple clang looks in `/usr/lib/c++/include` and `/usr/lib/c++/v1`. The patch makes homebrew's clang look into `/usr/local/c++/include` and `/usr/local/libc++/v1`. This *shouldn't* affect apple's clang at all.  This is only done if you install libc++, if you do install llvm *with* libc++ *and* clang from homebrew you *probably intend* for homebrew's clang to use homebrew's libc++ by default.
 
Note: `clang -stdlib=libc++ -I$LIBCXX_INCLUDE -L$LIBCXX_LIB` is enough (assuming `$LIBCXX_INCLUDE` and `$LIBCXX_LIB` point to  a valid libc++); `-nostdinc++` is not required. apple clang looks in `/usr/lib/c++/include` and `/usr/lib/c++/v1`.