What is the name of your custom table? Is it a global table? Or a table per site that your plugin is used in? As long as your table adheres to the WP table prefix ( like wp_ ) and includes the current site id (like wp_123_ for Site with ID: 123) then the Cloner will automatically clone it with that site and all the rest of that site's tables. Otherwise, there is no way for the Cloner to know about it, and a custom table could have a nearly infinite number of possible names to guess at. If you follow the convention wordpress uses for it's own individual site tables per site, the Cloner should have no problem automatically cloning those custom tables along with the standard ones. Hopefully that helps.
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