I am using cloner to to clone sites in a mu environment.
It looks like it sometimes does not copy the widget areas. But sometimes it works.
In addition I seem to get this error every time if I clone starting from the site list in the network admin.
However, it seems to work if you start from the dashboard of the site that you want to clone from.
Took me a while to discover this. Seems like a bug.
[Mon May 25 10:30:06.300045 2015] [:error] [pid 4314] [client 220.127.116.11:33892] WordPress database error Table 'wpone.wp_mcc_nbt_relationship' doesn't exist for query DELETE FROM wp_mcc_nbt_relationship WHERE blog_id = 0 made by do_action('wp_ajax_copier_process_copy_action':wink:, call_user_func_array, copier_process_ajax_template, copier_process_copy, Site_Copier_Settings->copy, switch_theme, do_action('switch_theme':wink:, call_user_func_array, MCC_NBT_Integrator->delete_blog_relationships_on_switch_theme, Multisite_Content_Copier_NBT_Model->delete_relationships, referer: https://testsite.writeboost.com/wp-admin/