Create an add-on to allow running the Cloner from the command line
This would allow you to use the php command from scripts to run the cloner with passed in parameters necessary to control cloning.
Thanks for the input @Samuel! We don't have an official API baked into it, BUT - the Cloner is rich with hooks and we built it specifically around the idea of a cloning pipeline that can be wired into from other plugins. It is VERY easy to use the Cloner's engine from anywhere within WP (or even outside WP if you load / include the main WP load file). Our own add-ons (especially Registration Templates) use the same mechanisms that are available to all plugins to tap into it / extend it / leverage it.
Samuel Arendt commented
Or even an API to integrate with other plugins.
Donald Overlander commented
Yes please, I am already scripting to wp-cli for a competing plugin that supports it - but would MUCH rather use NS Cloner. This is SERIOUSLY the only thing keeping a "university" sized project away.
We would also wish to use this cloner from our PHP applications. We do not want to use the admin interface we just wish to clone automatically.
Extending to Wordpress CLI (http://wp-cli.org/) would be great. This would allow us to write scripts to bulk create sites.