Pathologic was missing because of a .git folder inside.

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

name: Crop API
description: 'Provides storage and API for image crops.'
# core: 8.x
package: Media
type: module
dependencies:
  - image
  - user

# Information added by Drupal.org packaging script on 2017-04-01
version: '8.x-1.2'
core: '8.x'
project: 'crop'
datestamp: 1491032886