Pathologic was missing because of a .git folder inside.
[yaffs-website] / console /
drwxr-xr-x   ..
-rw-r--r-- 2911 aliases.yml
drwxr-xr-x - chain
-rw-r--r-- 1182 config.yml
-rw-r--r-- 400 phpcheck.yml
-rw-r--r-- 1304 router.php
-rw-r--r-- 815 site.mode.yml
drwxr-xr-x - sites