Revert "protobuf: Clean up and update to version 2.6.1."

This reverts commit 18b306b0414c13b5584c2325e9a01e065d715498. Protobuf
releases are generally not very backwards compatible and likely to
break lots of stuff. E.g.

  http://hydra.nixos.org/build/17535340
  http://hydra.nixos.org/build/17535640
  http://hydra.nixos.org/build/17536998
  http://hydra.nixos.org/build/17536170

See also b851e970daee1cd4a6b6977c9f67ed16cefc1229.