Just tested it, and the current quarry will do infinite cobblegen if set up right, but it only goes back to clear up the new cobble when it gets to the same x,z coord on the current mining layer, so it will mine the whole lot out even with cobble gen. Not sure what it does when it reaches bed rock though. Infinite water is however an issue, but the removal of lava should prevent cobble gen as lava is not infinite.
It may be that the quarry will always have to ignore water, or make it ignore it when the block under it isnt water. Infinite pools can olny be 1 deep, so dig out the next layer, let the water flow, then go back for it once the infinite mechanic is broken by flowing water blocks under it.
It may be that the quarry will always have to ignore water, or make it ignore it when the block under it isnt water. Infinite pools can olny be 1 deep, so dig out the next layer, let the water flow, then go back for it once the infinite mechanic is broken by flowing water blocks under it.