I am having trouble after trying to reinstall over a broken installation and getting the integrity check error on my .user.ini and .htaccess files. When I run the occ update htaccess command I get the following error:
Error updating .htaccess file, not enough permissions or "overwrite.cli.url" set to an invalid URL?
I have checked my config file though and there is no overwrite.cli.url set there. I do remember seeing this setting in my conf files before I reinstalled things but I don’t see it any longer.
I have also tried using the trick mentioned by @JasonBayton but it is not working for me. Disabling integrity check does prevent the message in my admin settings overview section but it doesn’t prevent the notification popping up.