This question is for the developer. Firstly, I appreciate your work on this plugin, I use it on all my sites. I think this should be a built-in option in WP core. :-)
I just ran into a conflict though with the Cart66 ecommerce plugin. Their plugin uses the "get_permalink()" function in order to create a hidden input field for a paypal checkout form. After much back and forth, we figured out that the Paypal Instant Payment Notifications (IPNs) were not working because the "notify_url" field was output with a value of "/store/ipn/" instead of the correct "http://sitename.com/store/ipn/".
Is this something that could be resolved with your plugin? The Cart66 folks say they can't change their code. I modified their plugin code to get it working for now, but of course that's a major problem going forward because eventually we'll need to update the plugin and my edits will get removed.
I'd really like to avoid disabling the Root Relative URLs plugin at this point, so I'm hoping somebody has an idea...
Thanks again for your work!