Preheat the oven to 350ºF and line a baking sheet with parchment paper.
Place softened butter in a mixer bowl, add white and brown sugar. Beat on high speed with the paddle attachment until fluffy.
Add applesauce and vanilla extract, mix on low speed just until combined. Don't worry if it curdles a little.
Add sifted flour, baking soda and sea salt and mix with a spoon until combined. Don’t overmix the dough at this point.
Add mix-ins: chopped chocolate, chocolate chips, pretzel twists, chopped candies, reserving about ½ cup for sticking on top of cookies. Mix again. Refrigerate the dough for 30 minutes.
With an ice cream or cookie dough scoop, place balls of dough on the lined baking sheet, leaving enough space for the cookies to spread while baking.
Press the reserved mix-ins onto the tops of the cookie dough balls, making sure the mix-ins are evenly distributed among them.
Bake for 10-12 minutes until slightly golden on top and around the edges. Remove from the oven and sprinkle with salt flakes. You can slightly push the uneven edges with a spatula if you want a perfectly shaped cookie.
Leave the cookies on the baking sheet for 5 minutes then transfer to the cooling rack with a spatula and let cool completely. Hot cookies will be very soft and crumbly so be careful not to break them.
Notes
To make the chopping of candies easier refrigerate them for 1 hour.
To store: Store kitchen sink cookies in an airtight container at room temperature for up to 3 days.
To freeze the dough: Scoop the dough onto a parchment-lined baking sheet and place it in the freezer for about an hour. Then, transfer the frozen dough balls to a freezer-safe container or bag and freeze for up to 2 months. Bake them according to the recipe instructions, adding a few extra minutes to the baking time.
To freeze baked cookies: Allow the cookies to cool completely and then store them in an airtight container or freezer-safe bag for up to 3 months. Thaw at room temperature before serving.