I’m a little late to respond, but since this is still happening with the release version of Xcode 10—and since I just got around to installing it—I’m hoping this might help you. In my case, the new build system was passing relative paths to clang when composing -i and -isystem switches, which was causing it to choke. This was an oversight on my part, as I supplied relative paths in my .xcconfig files when generating SYSTEM_HEADER_SEARCH_PATHS and friends; apparently, the older build system would silently convert these to absolute paths before passing them on, thus masking the problem. Switching to absolute paths solved the problem (though it introduces a different problem re: .xcconfig sharing, but I’m giving up and moving to CMake, anyway—it gets tedious maintaining all these .xcconfigs, .props, and make files).