I have the same Idea and just removed it… Now it is stopps with next folder:
Could not rmdir: /var/www/nextcloud/updater/../3rdparty
In my case root folder of nextcloud belongs to root, as it made per script:
# ls -la
total 116
drwxr-xr-x 13 root www-data 4096 May 7 16:37 .
drwxr-xr-x 6 root root 4096 Apr 27 20:23 ..
I changed it to www-data and now it works…
# sudo chown www-data:www-data ../nextcloud
#ls -la ../
total 24
...
drwxr-xr-x 13 www-data www-data 4096 May 7 16:37 nextcloud
Now is the question: why correct strong permissions will break my web update?
UPDATE:
It is unbelievable… It is finished with same “core/shipped.json is not available” error!
What I did wrong?