Unfortunately, this fine plugin (Add Clone Sites for WPMU (batch)) doesn’t do that…
From its FAQ:
Why can’t I clone the main site?
I chose not to because the main site can be slightly different in structure than a new network site.
Albeit a little chaotic and difficult to search, there’s very good info about MS in WordPress official forum.
I won’t do a deep search for you, but if you do, and find a nice method, please post it here 🙂
From a fast search I found this support thread, where the great andrea_r has this to say:
Manual way:
http://bavatuesdays.com/importing-a-single-wp-blog-to-a-wpmu-installation/
which is for importing an existing standalone blog into a network, but
can also be used the other way, or to help you figure out how to dupe
blogs manually within a network.
WP Multisite Replicator.
She also has this premium plugin but seems that it doesn’t replicates the main site neither.
A search in their support forum may be worthwhile.
Finally, I know that this other one, premium as well, does it: BackupBuddy.
The actual version is still in Beta stage regarding Multisite, and have some glitches (nothing grave) when exporting.
But apart export/import, it also has a duplicate option, that I just tested.
I did it with the Main Site in a local MS and seems ok.
