SpiderOak ONE and Groups are intended to back up user files, not to clone or back up systems. Our design works well for the intended use, but any rsync-like tool that runs in userspace would be a bad choice to make a system clone. Cloning your system is an excellent idea; we're just not a good tool for that.
We suggest a two pronged approach: clone your system, then back up your files. Get your system how you want it, then use a system clone tool. One popular choice is the open source Clonezilla:
Store the clone in a safe place, such as on an external drive that is then stored away for safekeeping. Once the clone is made, all you have to do is have SpiderOak ONE or Groups back up your user files.
In case of disaster, restore the system using your system clone tool, your user files from SpiderOak ONE or Groups, and you are done.