Remove checkpoints v2

We're reassessing checkpoints v2 and working on a v1.1 with the parts that worked. We should be able to safely switch back to checkpoints v1 at this time (transcripts, commands etc. will fall back to v2 as long as the v2 ref is around).

We will keep the v2 checkpoint ref around for a bit while we work on fully migrating back to v1 for those checkpoints that were in v2-only mode.