sql/migrate: handle partially applied checkpoint files #989

Job	Run time
integration-maria103	1m 44s
integration-maria107	1m 30s
integration-mysql56	1m 31s
integration-mysql57	1m 33s
integration-maria102	1m 26s
integration-mysql8	2m 1s
integration-cockroach	1m 35s
integration-postgres10	1m 43s
integration-postgres11	1m 45s
integration-postgres12	1m 54s
integration-postgres13	1m 41s
integration-postgres14	1m 52s
integration-postgres15	1m 50s
integration-postgres-ext-postgis	1m 46s
integration-sqlite	58s
integration-tidb5	1m 59s
integration-tidb6	2m 10s
	28m 58s

Provide feedback