Revert "Add a read-layer option to ruminating layers."

This reverts commit 9a6ead95d5807e7c42953bc9d4068e965b7b068e.

We added this feature only due to our own confusion.

Conflicts:

        src/flatland/jiraph/ruminate.clj
Rename the layers that ruminate wraps.

Rather than input/output, @ninjudd thinks primary/secondary is clearer.