Update //third_party/protobuf to version 3.

third_party/protobuf/protobuf_nacl.gyp

Index: third_party/protobuf/protobuf_nacl.gyp
diff --git a/third_party/protobuf/protobuf_nacl.gyp b/third_party/protobuf/protobuf_nacl.gyp
index ae37f2f01502d0d699357c10bf1dd1c235d6a69f..6fb3ac216ce291f65900edecd91ed6b72536425d 100644
--- a/third_party/protobuf/protobuf_nacl.gyp
+++ b/third_party/protobuf/protobuf_nacl.gyp
@@ -15,7 +15,6 @@
         'build_glibc': 0,
         'build_newlib': 0,
         'build_pnacl_newlib': 1,
-        'config_h_dir': '.',
       },
       'pnacl_compile_flags': [
         # This disables #warning in hash_map/hash_set headers which are
@@ -28,6 +27,12 @@
       'includes': [
         'protobuf_lite.gypi',
       ],
+      'defines': [
+        # protobuf requires these to be set manually, as it no longer
+        # uses config.h
+        'HAVE_ZLIB',
+        'HAVE_PTHREAD',
+      ],
     },  # end of target 'protobuf_lite_nacl'
   ]
 }