Pathologic was missing because of a .git folder inside.
[yaffs-website] / web / modules / contrib / pathologic / src /
drwxr-xr-x   ..
-rw-r--r-- 2512 PathologicSettingsCommon.php
-rw-r--r-- 1619 PathologicSettingsForm.php
drwxr-xr-x - Plugin
drwxr-xr-x - Tests