Minor Net::Init refactoring

This PR is purely for refactoring; it's not intended to change any behavior whatsoever.  It makes the `Net::Init` method a bit more readable (imo) by (1) changing the single-character loop index var names (which I use constantly, no offense intended) to more meaningful ones like `layer_id` or `bottom_id`, and (2) factoring out some of `Init` into separate methods `AppendBottom` and `AppendTop`.  `AppendBottom` is called once for each bottom blob, `AppendTop` is called once for each top blob or input blob (merging the common setup between inputs and normal top blobs).

I will follow up with other PRs built on top this one, but I'm PRing this first to make it easier to see what has actually changed with those further PRs in terms of behavior, vs. just changes due to refactoring.  Feel free to ignore this PR until those followups appear.