Fix `with_data` handling in test-migrations.

Two issues with the existing code:

1) migrate-down wasn't respecting the `with_data` flag

2) migrate-up was not actually migrating unless `with_data` was True.
The correct behavior is to always migrate up, but only run checks when
`with_data` is set.

Change-Id: I781fa4796908bea684d4499fa9ff5e4d7a18fbd4
Merge "Fix `with_data` handling in test-migrations."