The only way to do this right now is to manually go through all the migrations. That is, you must run the migration command in each of your subfolders:
php artisan migrate --path=/app/database/migrations/relations php artisan migrate --path=/app/database/migrations/translations
However, what you can do is easily expand the artisans system to write your own migrate command, which will iterate over all the folders in the migration folder, create these commands for you, and run them.
You can also just write a shell script if you don't want to do this through artisan
Edit: for Laravel> = 5.0, the correct commands for migrating migration files in subdirectories are:
php artisan migrate --path=/database/migrations/relations
php artisan migrate --path=/database/migrations/translations
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