Custom (cck) fields are being ignored during the migration using migration-tools 4.x. Only title and body is imported. How do I fix this?
What version of migrate_upgrade are you using? I see things like

      plugin: migration
      migration:
        - d6_filter_format
        - d7_filter_format


there, but --configure-only should have generated

      plugin: migration
      migration:
        - upgrade_d6_filter_format
        - upgrade_d7_filter_format