Prepare to remove a bunch of proto.h includes from tensorflow/core headers

The goal is to make kernels mostly independent of proto headers, which will let
us lock down our .so imports.  This CL does not remove any actual headers, but
changes a bunch of files so that header removal is possible in a followup CL.
It also marks the headers that will be removed with

    // TODO(b/62899350): Remove

RELNOTES: n/a
PiperOrigin-RevId: 160552878