What to do with hidden files in Drupal 8 minor core upgrade? Step 3 of https://api.drupal.org/api/drupal/core!UPGRADE.txt/8 says


  Also remove all of the files in the top-level directory, except any that you added manually.


it doesn't exclude or include hidden files explicitly, so my logic would say 'all' includes hidden files.

later it says

cp -R drupal-x.y.z/* drupal-x.y.z/.htaccess /path/to/your/installation


which does not copy any hidden files except .htaccess.

This would suggest not to delete the old hidden top level files. On the other hand the new version/patch of Drupal 8.y.z comes with (new?) hidden files.

So my question is: what is the correct way to handle top level hidden files other than .htaccess while upgrading Drupal 8?
TL:DR;
You should delete all files hidden and not hidden that you didn't place there yourself.

Drupal core has a lot of hidden files, which are used when developing Drupal itself (git, lint and possibly more) but none of those are needed or relevant for running a Drupal site in production. They are highly relevant when you are working on Drupal itself.

The only hidden file you need for a production site is the .htaccess, if you have more than that they are safe to delete.