Update //third_party/protobuf to version 3.

third_party/protobuf/patches/0001-ignore-option-retain-unknown-fields.patch

+--- protobuf-cleaned/src/google/protobuf/descriptor.cc  2015-12-30 13:21:46.000000000 -0800
++++ protobuf-patched/src/google/protobuf/descriptor.cc  2016-03-31 13:25:26.840024811 -0700
+@@ -5591,6 +5591,18 @@
+                         "\"uninterpreted_option\".");
+   }
+ 
++  // TODO(xyzzyz): remove when all uses in Chromium are removed
++  if (uninterpreted_option_->name(0).name_part() == "retain_unknown_fields") {
++    // Chromium patch to protobuf used to introduce a retain_unknown_fields
++    // option that would make the protobuf_lite runtime retain unknown fields
++    // just like the protobuf_full would. A newer upstream version of protobuf
++    // retains these unknown fields even in lite runtime, so the option is no
++    // longer necessary. Therefore, we ignore this option, and when we remove
++    // all the occurrences of the option from Chromium, we can remove this
++    // ignore.
++    return true;
++  }
++
+   const Descriptor* options_descriptor = NULL;
+   // Get the options message's descriptor from the builder's pool, so that we
+   // get the version that knows about any extension options declared in the