Drush migration no longer working in 8.5
Ok answering this myself. I keep forgetting that Drupal often introduces breaking changes and treats comments as code. It looks like the annotation changed in 8.5

What was in 8.4:

/**
 * Drupal 7 file_entity source from database.
 *
 * @MigrateSource(
 *   id = "file_entity",
 *   source_provider = "file"
 * )
 */


in 8.5 should now be:

/**
 * Drupal 7 file_entity source from database.
 *
 * @MigrateSource(
 *   id = "file_entity",
 *   source_module = "file",
 * )
 */