Pathologic was missing because of a .git folder inside.
[yaffs-website] / web / modules / contrib / pathologic /
drwxr-xr-x   ..
-rw-r--r-- 545 README.txt
drwxr-xr-x - config
-rw-r--r-- 3415 pathologic.api.php
-rwxr-xr-x 194 pathologic.info.yml
-rw-r--r-- 2524 pathologic.install
-rw-r--r-- 218 pathologic.links.menu.yml
-rw-r--r-- 17220 pathologic.module
-rw-r--r-- 17236 pathologic.module.orig
-rw-r--r-- 226 pathologic.routing.yml
drwxr-xr-x - pathologic_test
drwxr-xr-x - src