Using a site with a custom public folder is a pain. While core Joomla, Akeeba extensions, and most correctly written third party extensions will work just fine, there are a number of popular third party extensions which don't. Most of these extensions do something really wrong, like trying to place web-accessible files inside their directories, Joomla's tmp or cache folder (instead of placing these files in the media folder which has been available for this purpose since Joomla! 1.5.0 released in 2007), or use web-accessible .php files instead of com_ajax (which has been available for this purpose since Joomla! 3.2 released in 2012).

Moreover, the custom public folder feature is incompatible with Windows computers and servers due to limitations of PHP itself under this platform.

Either way, you will eventually need to convert a site that has a custom public folder to one that does not.

This is very simple with Akeeba Backup, meaning that you can back up a site that uses custom public folders on a Linux-powered server and restore it on your Windows computer without having to put any thought in it — that's the entire point of us supporting this new Joomla feature, after all.

Take a backup of the site.

Completely empty the public folder (if it's not already empty).

Put the backup archive and kickstart.php in there.

Run the restoration, as per the documentation and video tutorials covering the use case of restoring a site to any server.

You will see an additional step called Public Folder. When you reach it, you will be told that your configuration is incompatible with the public folder feature and the feature will be disabled when you continue. Perfect! That's what we want! Click on Next.

This will copy and custom files and folders you previously had in your custom public folder into the site's main folder. It will also copy the .htaccess files you had in your public root and its administrator subdirectory into the respective folders under your restored site. These files will also be automatically edited to reflect the changes in the Joomla installation folder, and public folder.