Click on the stones and crystals to harvest them. You will need to clear the area a bit before new things spawn. Clicking on the pile of rocks in the bottom left allows you to play a mini game. Use left and right arrows to move your character, avoid large rocks and collect the mini Stone and Crystal items. Quarries cost stone, alchemists cost crystals. Farms cost stone and boost other items.
Challenge 1: Obtain 50 Crystals [Alchemist's Wonder] Challenge 2: Obtain 500 Crystals [Shining Wealth] 42nd, and final, project for Scratch - just a quick idle game.