So it turns out that my own stupidity (or smart arse idea!) caught me out. I install drupal core in a separate directory out of the web root (docroot!) directory and symlink back to it. My web root looks a little like this:
lrwxrwxrwx autoload.php -> /var/www/src/drupal-8.x/autoload.php
lrwxrwxrwx core -> /var/www/src/drupal-8.x/core
-rw-r--r-- .htaccess
lrwxrwxrwx index.php -> /var/www/src/drupal-8.x/index.php
drwxr-xr-x modules
drwxr-xr-x profiles
-rw-r--r-- robots.txt
drwxr-xr-x sites
drwxr-xr-x themes