Restore this change but with a clean of the generated dirs first so
that we avoid trying to apply a patch on top of an already patched src.
This reverts commit 0f384158fc.
Adds means of patching our shaded protobuf. Does it using
the Anoop patch attached to HBASE-15789 that adds ByteInput
to protobuf. This patch gets applied after protobuf has been
downloaded, relocated, and then unpacked over src/main/java.
Also fixes a few small build WARNINGs because of duplicate
mentions of dependencies.