redirect to root

Hi! I’ve successfully prepared the website in a /wordpress subfolder,and prefer to leave it there rather than put it in my root folder. I’ve successfully copied .htaccess to root and copied and modified index.php to root so that when I type in http://www.mysite.com the /wordpress subfolder does not show in the URL. However – it still shows in all pages except my homepage. I’ve read somewhere that some themes are hard-wired to do this. Is this true of Agama? If so, is there a workaround so I get get rid of the /wordpress in the URLs for ALL pages?
Thank you.