Move the migration helper scripts to commands

Running as a "[nested command](https://github.com/SURFnet/Stepup-Middleware/blob/7c1365ae00f6a17b0f6b6d3e4ecb657b1ef29f6f/src/Surfnet/StepupMiddleware/MiddlewareBundle/Console/Command/MigrationsDiffDoctrineCommand.php#L37)", because the [original command is so tightly coupled to InputInterface](https://github.com/doctrine/DoctrineMigrationsBundle/blob/81575a4316951125ce408c70f30547c77d98f78a/Command/MigrationsDiffDoctrineCommand.php#L46).

Ready for review @DRvanR.