Admin Tools will automatically detect that you are using a custom public folder. This means that the the .htaccess and web.config files created by various features (.htaccess Maker, Web Config Maker, Administrator Password Protection, Emergency Off-line Mode) will be created in the public folder, not the root of your site.

This also means that if you have such a site you need to read the troubleshooting information instructing you to edit, rename, or delete these files as though they are referring to files under your public folder, not under the folder where your site files are stored into.

Please note that the nginx.conf file generated by the NginX Conf Maker IS NOT placed in the public folder; it is still placed inside the folder where you have put your Joomla installation's files. This is deliberate. The nginx.conf folder is best placed in a folder outside of the web root as it only ever needs to be explicitly included by your NginX server's configuration file (you tell the server where to find it, as opposed to .htaccess and web.config where the server specifies where the file must be placed into).

Important notes for CLI commands

Please note that due to an issue in Joomla, CLI commands will by default try to generate / operate on files inside the folder where Joomla's files are installed, not the public folder where these files need to be. The affected commands are:

You can fix this problem by creating the file cli/defines.php under the folder you have installed Joomla in (e.g. /opt/joomla/cli/defines.php) with the following contents:

<?php
define('JPATH_PUBLIC', '/var/www/html');

Where /var/www/html is the absolute filesystem path of your custom public directory.

This solution is perfectly compatible with Akeeba Backup 9.8.1 or later. When restoring your site to a different location or server this file will be automatically updated.