After updating to the latest version it seems that it's no longer possible to hide folders/files using the customizables/config.php
I read the changelog which said that the setting I was using, $config['app']['hidden_folder_names'] had been deprecated and that I should use $config['app']['hidden_file_names'] instead. Neither of them are doing anything though. Neither is the setting in changelog $config['app']['excluded_filenames'] which actually isn't even in the documentation.
Customer support service by UserEcho