Update the checkpoints index file in CheckpointProto before actually deleting files.

Current order of execution is:
1. Save the new checkpoint
2. Delete old checkpoint files
3. Update the checkpoint proto

If the job is preempted after 2, then the checkpoint proto is left pointing to a deleted file.

It is better to update the checkpoint proto first:
1. write new checkpoint
2. update checkpoint proto
3. delete old checkpoint

I added tests to cover checkpoint proto in 168744975 and they are not failing with this change.

PiperOrigin-RevId: 169161095