Fix nostdincxx

This fixes an issue that Marcos Scriven found and discussed on the mailing list.

It undoes this comment from @ehsan https://github.com/kripken/emscripten/commit/74a7e8e which was part of pull request #478.

This doesn't change anything for me on OS X, but part of that might be that the target triple is not native, so I don't have directories for that stuff anyway. If that's the case, someone might check this on x86-linux.

I don't see any new warnings or spew like @ehsan was seeing before from having this enabled all the time.