Include stlport through -isystem instead of -I.

build/common.gypi

 # Copyright (c) 2012 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.
 
 # IMPORTANT:
 # Please don't directly include this file if you are building via gyp_chromium,
 # since gyp_chromium is automatically forcing its inclusion.
 {
   # Variables expected to be overriden on the GYP command line (-D) or by
   # ~/.gyp/include.gypi.
@@ skipping 3797 matching lines @@
             'cflags!': [
               # Clang doesn't seem to know know this flag.
               '-mfpmath=sse',
             ],
             'cflags_cc': [
               # See the comment in the Mac section for what it takes to move
               # this to -std=c++11.
               '-std=gnu++11',
             ],
           }],
-          ['clang==1 and OS=="android"', {
-            # Android uses stlport, whose include/new defines
-            # `void  operator delete[](void* ptr) throw();`, which
-            # clang's -Wimplicit-exception-spec-mismatch warns about for some
-            # reason -- http://llvm.org/PR16638. TODO(thakis): Include stlport
-            # via -isystem instead.
-            'cflags_cc': [
-              '-Wno-implicit-exception-spec-mismatch',
-            ],
-          }],
           ['clang==1 and clang_use_chrome_plugins==1', {
             'cflags': [
               '<@(clang_chrome_plugins_flags)',
             ],
           }],
           ['clang==1 and clang_load!=""', {
             'cflags': [
               '-Xclang', '-load', '-Xclang', '<(clang_load)',
             ],
           }],
@@ skipping 584 matching lines @@
               # toolchain (circa Gingerbread) will exhibit strange errors.
               # The include ordering here is important; change with caution.
               ['use_system_stlport==1', {
                 'cflags': [
                   # For libstdc++/include, which is used by stlport.
                   '-I<(android_src)/bionic',
                   '-I<(android_src)/external/stlport/stlport',
                 ],
               }, { # else: use_system_stlport!=1
                 'cflags': [
-                  '-I<(android_stlport_include)',
+                  '-isystem<(android_stlport_include)',
                 ],
                 'ldflags': [
                   '-L<(android_stlport_libs_dir)',
                 ],
               }],
               ['target_arch=="ia32"', {
                 # The x86 toolchain currently has problems with stack-protector.
                 'cflags!': [
                   '-fstack-protector',
                 ],
@@ skipping 1071 matching lines @@
     # settings in target dicts.  SYMROOT is a special case, because many other
     # Xcode variables depend on it, including variables such as
     # PROJECT_DERIVED_FILE_DIR.  When a source group corresponding to something
     # like PROJECT_DERIVED_FILE_DIR is added to a project, in order for the
     # files to appear (when present) in the UI as actual files and not red
     # red "missing file" proxies, the correct path to PROJECT_DERIVED_FILE_DIR,
     # and therefore SYMROOT, needs to be set at the project level.
     'SYMROOT': '<(DEPTH)/xcodebuild',
   },
 }