Ignore modules already managed by Composer

If drupal/commerce depends on drupal/entity then Composer will download the Entity module and place it in the appropriate place.
On the next run Composer Manager will discover the new Entity module, and if it has a composer requirement, start managing it (by adding it to the replace section of the composer.json file for example, as needed by #2595225: Add the managed extensions to the replace list). This will confuse Composer, and result in the Entity module simply being removed.

Solution: Ignore extension packages from modules already managed by Composer. This makes total sense.