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IIRC Exterminatus that geologically destabilizes a planet into a Mustafar-ian type world would essentially replenish a lot of the stones/gems/minerals/etc. I just can't remember what novel it was in.
However, I do become rather imaginative while on the toilet taking a crap, so please, take the above with a very large grain of salt. It might be a poop-time rambling of mine that got stuck in my head.