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It's important to note that the upgrade process actually is extensible - if you define a migration .yml with migration_tags of 'Drupal 6' and/or 'Drupal 7', the migration will be executed as part of the upgrade. The issue with the hardcoded list of migrations (and their related source and destination modules) only affects reporting - the list of available and "missing" migrations on the confirmation page in the upgrade UI. Your migration may not be listed there, but it will actually be executed.