Pathologic was missing because of a .git folder inside.

[yaffs-website] / web / modules / contrib / migrate_upgrade / migrate_upgrade.info.yml

name: Drupal Upgrade
type: module
description: 'Drush support for direct upgrades from older Drupal versions.'
package: Migration
# core: 8.x
dependencies:
  - drupal:migrate (>=8.2)
  - drupal:migrate_drupal
  - migrate_plus:migrate_plus
  - drupal:dblog

# Information added by Drupal.org packaging script on 2016-10-11
version: '8.x-3.0-rc1'
core: '8.x'
project: 'migrate_upgrade'
datestamp: 1476200662