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

third_party/libc++/libc++.gyp

 # 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.
 
 {
   'variables': {
     'libcxx_root': '../../buildtools/third_party/libc++',
   },
   'targets': [
     {
       'target_name': 'libcxx_proxy',
       'type': 'none',
       'toolsets': ['host', 'target'],
       'dependencies=': [
         'libc++',
       ],
       # Do not add dependency on libc++.so to dependents of this target. We
       # don't want to pass libc++.so on the command line to the linker, as that
       # would cause it to be linked into C executables which don't need it.
       # Instead, we supply -stdlib=libc++ and let the clang driver decide.
       'dependencies_traverse': 0,
       'variables': {
         # Don't add this target to the dependencies of targets with type=none.
         'link_dependency': 1,
       },
       'all_dependent_settings': {
         'target_conditions': [
           ['_type!="none"', {
-            'cflags': [
+            'cflags_cc': [
+              '-nostdinc++',
               '-isystem<(libcxx_root)/trunk/include',
               '-isystem<(libcxx_root)/../libc++abi/trunk/include',
             ],
-            'cflags_cc': [
-              '-nostdinc++',
-            ],
             '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:
               # https://code.google.com/p/gyp/issues/detail?id=315
               '-Wl,-R,\$$ORIGIN/lib/',
             ],
             'library_dirs': [
               '<(PRODUCT_DIR)/lib/',
@@ skipping 35 matching lines @@
         'trunk/src/stdexcept.cpp',
         'trunk/src/string.cpp',
         'trunk/src/strstream.cpp',
         'trunk/src/system_error.cpp',
         'trunk/src/thread.cpp',
         'trunk/src/typeinfo.cpp',
         'trunk/src/utility.cpp',
         'trunk/src/valarray.cpp',
       ],
       'cflags': [
+        '-fPIC',
+        '-fstrict-aliasing',
+        '-pthread',
+      ],
+      'cflags_cc': [
+        '-nostdinc++',
         '-isystem<(libcxx_root)/trunk/include',
         '-isystem<(libcxx_root)/../libc++abi/trunk/include',
-        '-fPIC',
-        '-fstrict-aliasing',
-        '-nostdinc++',
-        '-pthread',
         '-std=c++11',
       ],
       'cflags_cc!': [
         '-fno-exceptions',
         '-fno-rtti',
       ],
       'cflags!': [
         '-fvisibility=hidden',
       ],
       'defines': [
@@ skipping 10 matching lines @@
       'libraries': [
         '-lc',
         '-lgcc_s',
         '-lm',
         '-lpthread',
         '-lrt',
       ],
     },
   ]
 }