My personal best guess on Clarion, was that it was a failed scuttleing attempt that left it in the hands of the republic. Unless Devlin Stone is/was WoB of course, but that is one theory I do not subscribe to, my gut says it just doesn't feel quite right. I think that, if it was a WoB super weapon, and it got hit by the liberation forces before it could get used, the blakist forces would have tried to destroy it before it got captured. However, history is full of lucky breaks for attackers, when one side tried to destroy something, and for whatever reason it failed, leaving enough there to be captured and, at the very least, reverse engineered.