Renumber CHECKPOINT_* flags.

Commit 7dbb6069382 added a new CHECKPOINT_FLUSH_ALL flag. As that
commit needed to be backpatched I didn't change the numeric values of
the existing flags as that could lead to nastly problems if any
external code issued checkpoints. That's not a concern on master, so
renumber them there.

Also add a comment about CHECKPOINT_FLUSH_ALL above
CreateCheckPoint().