Pathologic was missing because of a .git folder inside.

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

name: Typogrify
type: module
description: 'Adds typographic refinements.'
package: 'Input filters'
# core: 8.x
# project: typogrify

dependencies:
  -  filter

# Information added by Drupal.org packaging script on 2016-11-02
version: '8.x-1.0-alpha1'
core: '8.x'
project: 'typogrify'
datestamp: 1478050443