The Cloner tool is advertised as being ideal for creating a safe staging area, separate from your live site. Unfortunately, the way it is right now, it actually copies too much to make it that "safe".
If the site you are cloning has any plugins that push data to other places (i.e. Twitter), these things are all copied AND there is no way to indicate a site privacy lower than 'don't index' (despite using WPMU Dev's own Site Privacy tool on our install).
Would it be possible to have an additional checkbox (at least) to select whether plugins are cloned? This would at least allow for a copy of the site without the risk of plugins pushing data out from a staging site. I don't want to uncheck "Settings", as I assume this would affect more than just plugin settings.