Revert protobuf changes

Protobuf has been updated to 3.9.1,  we can undo the changes made to
make kythe work with old protobuf.  Partially reverts
I5df762b549ba406c23e05f2836acb8f5bc5f0120 and
I46ca627323e8bf01311aa0b6e0ef44250777faa6.

Bug: 140626397
Test: builds
Change-Id: I1af08b94b83f48570f016720cc4250186c6bf2f6
2 files changed