In a mixing bowl, cream together 1 cup of softened unsalted butter and 1 cup of granulated sugar until light and fluffy, about 3 minutes. Gradually mix in 2 cups of all-purpose flour and a pinch of salt until just combined. Wrap the dough in plastic wrap and refrigerate for at least 30 minutes.

Preheat the oven to 350°F (175°C) while the dough chills. Prepare a muffin tin by lightly greasing it or using muffin liners.

Scoop the chilled dough into 1.5-inch balls and place them in the prepared muffin tin. Press down in the center of each ball to create a cup shape. Bake for 10-12 minutes until edges are golden and centers are puffed.

In a bowl, beat together 8 ounces of cream cheese, 1/2 cup of powdered sugar, 1 teaspoon of vanilla extract, and 1 egg yolk until smooth. This is the cheesecake filling.

Once the cookie cups have baked and slightly cooled, press down the centers if puffed. Spoon about 1-2 teaspoons of cream cheese filling into each cup. Return the filled cups to the oven for an additional 5 minutes.

After baking, let the cookies cool for about 10 minutes before transferring to a wire rack. Drizzle warm caramel sauce on top and sprinkle with sea salt flakes. Refrigerate for at least 1 hour before serving.