preheat oven to 350F
grease or spray a muffin pan
Slice about 1/2 inch of dough. Using your fingers, take each slice and push it into the bottom and up the sides of each muffin mold. You'll want to press firmly to make sure its adhered to all sides.
Bake for 10-12 minutes or until cookies are slightly golden. Depending on your oven, it could take more or less, so watch carefully to make sure they don't burn.
Take out of oven and create a cup by pushing the end of shot glass into each muffin cup (you could also use the bottom of a spice jar or wooden spoon. you just need to push the middle of each cookie back down to create a "cup")
Allow to cool slightly and then using a butter knife, carefully take each cookie out of the muffin tin.
Heat the caramel with the water in a microwave. (use more or less water depending on the consistency of the caramel) Heat in intervals of 30 seconds, stirring between heating. It should take 2-3 times to be fully melted and creamy. Fill each cookie cup 2/3 full with caramel.
Place cookies in the fridge for about 20 minutes to set the caramel. While caramel is setting, melt chocolate in the microwave, again in intervals of 30 seconds.
Take cookies out of fridge and pour chocolate to the top of each cookie. Sprinkle each cookie with a pinch of sea salt.
Cool cookies in the fridge to set chocolate and then store in an airtight container.