Pathologic was missing because of a .git folder inside.

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

name: Media entity document
description: 'Media entity local documents provider.'
type: module
package: Media
# core: 8.x
dependencies:
  - media_entity

# Information added by Drupal.org packaging script on 2016-08-03
version: '8.x-1.1'
core: '8.x'
project: 'media_entity_document'
datestamp: 1470211440