Fix below failure, and re-enable checkpoint-test in Evergreen and Makefile.am.
[2020/04/29 00:41:07.617] [1588120867:73151][19701:0x7f5e977f6700], t, WT_SESSION.commit_transaction: __wt_txn_set_commit_timestamp, 689: commit timestamp (0, 2) is less than the stable timestamp (0, 997): Invalid argument