I have a blog to convert to Multi Site and two blogs to integrate into it once Multi Site is enabled. The main site is installed at root and the secondary sites are installed in subdirectories. I need to activate Multi Site for subdirectory addon blogs not subdomain addon blogs so I can maintain the URL structures of the secondary blogs but I'm not given the option to setup Multi Site for subdirectories because "your blog is too old" (whatever that means). The blog is up to date (WP 3).
The primary blog is very big and popular so I don't want to put it offline while I re-install it. Is there a way around this? Can I edit the database somewhere and/or just replace certain files to get WordPress to allow me to setup Multi Site for subdirectories?