We have our multisite set up with subdomains. Our base site is on http://www.ourdomain.com and network sites have subdomains like test1.ourdomain.com test2.ourdomain.com etc.
When running the cloner the cloner tries to go to the url test1.www.ourdomain.com instead of test1.ourdomain.com - i.e. it is substituting in the whole url of the base site http://www.ourdomain.com into the url and therefore failing during the clone process.
If the site is set up with folders instead of subdomains it works perfectly, but we want to use subdomains for each site on the network. Is there a fix/workaround for this issue in your plugin?