As you pointed out, -isystem is a way for gcc process the include dirs system and unlike the -I directories, the -isystem tags will have warnings suppressed, and various other behaviors that you get from the system include paths.
Xcode may not make this obvious, but a gcc-like llvm-based compiler, provided with Xcode 4.3 , supports this function like gcc. This seems to be a common myth that it does not (no doubt because it was not in the past), and even CMake (2.8.7) still continues to avoid using the -isystem option with Xcode.
For those who create Xcode projects manually, the "header search paths" (as opposed to the "User header search paths") in the settings of your project will also work, as you already mentioned, and probably easier t use something like CMake to create your Xcode project.
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