Only add -isystem for libc++ for C++ files, not C files.

third_party/libc++/BUILD.gn

 # Copyright 2015 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
+# Used by libc++ and libc++abi.
 config("config") {
+  defines = [ "LIBCXX_BUILDING_LIBCXXABI" ]
   cflags = [
+    "-fPIC",
+    "-fstrict-aliasing",
+    "-pthread",
+  ]
+  cflags_cc = [
+    "-nostdinc++",
     "-isystem" + rebase_path("trunk/include", root_build_dir),
     "-isystem" + rebase_path("../libc++abi/trunk/include", root_build_dir),
-    "-fPIC",
-    "-fstrict-aliasing",
-    "-nostdinc++",
-    "-pthread",
     "-std=c++11",
-    "-DLIBCXX_BUILDING_LIBCXXABI",
   ]
 }
 
 shared_library("libc++") {
   sources = [
     "trunk/src/algorithm.cpp",
     "trunk/src/any.cpp",
     "trunk/src/bind.cpp",
     "trunk/src/chrono.cpp",
     "trunk/src/condition_variable.cpp",
@@ skipping 26 matching lines @@
     "//build/config/gcc:no_exceptions",
     "//build/config/gcc:symbol_visibility_hidden",
   ]
   configs += [
     ":config",
     "//build/config/compiler:no_chromium_code",
     "//build/config/compiler:rtti",
     "//build/config/sanitizers:sanitizer_options_link_helper",
   ]
 
-  defines = [ "LIBCXX_BUILDING_LIBCXXABI" ]
   ldflags = [ "-nodefaultlibs" ]
 
   # TODO(GYP): Remove "-pthread" from ldflags.
   # -nodefaultlibs turns -pthread into a no-op, causing an unused argument
   # warning. Explicitly link with -lpthread instead.
 
   libs = [
     "c",
     "gcc_s",
     "m",
     "pthread",
     "rt",
   ]
 
   # libc++abi is linked statically into libc++.so. This allows us to get both
   # libc++ and libc++abi by passing '-stdlib=libc++'. If libc++abi was a
   # separate DSO, we'd have to link against it explicitly.
   deps = [
     "//buildtools/third_party/libc++abi",
   ]
 }
 
 group("libcxx_proxy") {
   deps = [
     ":libc++",
   ]
   public_configs = [ ":link_helper" ]
 }
 
+# This config is only used by binaries and shared library targets.
+# //build/config/sanitizers:default_sanitizer_flags sets the include paths for
+# everything else.
 config("link_helper") {
   ldflags = [
     "-stdlib=libc++",
 
     # Normally the generator takes care of RPATH. Our case is special because
     # the generator is unaware of the libc++.so dependency. Note that setting
     # RPATH here is a potential security issue. See the following for another
     # example of this issue: https://code.google.com/p/gyp/issues/detail?id=315
     "-Wl,-R,\$ORIGIN/",
   ]
   lib_dirs = [ root_build_dir ]
 }