Bump protobuf dependency to 3.0.0-beta-3

This allows us to play with zero-copy and proto3 support for lite.
Unfortunately, it introduced some warnings, so deprecated warnings are
now ignored for benchmarks and interop-testing.
diff --git a/compiler/Dockerfile b/compiler/Dockerfile
index e25f285..a51aaca 100644
--- a/compiler/Dockerfile
+++ b/compiler/Dockerfile
@@ -2,7 +2,7 @@
 
 RUN scl enable devtoolset-1.1 'bash -c "cd /protobuf && \
     git fetch && \
-    git checkout v3.0.0-beta-2 && \
+    git checkout v3.0.0-beta-3 && \
     ./autogen.sh && \
     CXXFLAGS=-m32 ./configure --disable-shared --prefix=/protobuf-32 && \
     make clean && make -j$(nproc) && make -j$(nproc) install"'