Pathologic was missing because of a .git folder inside.

[yaffs-website] / web / modules / contrib / hacked / hacked.links.menu.yml

hacked.report:
  title: 'Hacked'
  description: 'Get a code hacking report about your installed modules and themes.'
  route_name: hacked.report
  parent: system.admin_reports
  weight: 10