Recompute auto-numbered reference listKeys when merging internalLists

This fixes some of the problems with pasting references.

It's a bit overzealous in that references get renumbered even when
replacing, which is unnecessary but doesn't actually have any
noticeable effect.

Unfortunately, the internal list state depends so much on the converter
having run that we now need to add yet another hack, to set the counter
to the appropriate value.

Change-Id: I3c6514ce600af4f4c037f419554d34b5a5c86a63
Merge "Recompute auto-numbered reference listKeys when merging internalLists"