Hi,
I understand the idea behind this new message
$strConfigDirectoryWarning = 'Directory [code]config[/code], which is used by the setup script, still exists in your phpMyAdmin directory. You should remove it once phpMyAdmin has been configured.'; //to translate
but what I find unfortunate is that, by adding this warning, we will discourage admins to use the web-based interface for ongoing configuration tasks which can be more frequent than just the initial installation.
Maybe verify whether the directory is writable and if so, produce a warning? This way the admin would just have to change permission.
Marc