Heat oven to 365 F. or 355 F. for convection ovens
Line 2 cookie sheets or baking pans with parchment paper or silicone baking mats.
In a small bowl, whisk together flours, baking soda and salt; set aside. In the bowl of a stand mixer, or a large mixing bowl, cream together butter, shortening, granulated sugar, molasses, and vanilla on high speed until creamy and combined, about 2 minutes.
Add eggs and yolk, one at a time, mixing well after each addition. Stir in flour mixture on low speed or by hand. To prevent dry, tough cookies, do not over mix. Stir in chocolate chips.
Use a cookie scoop to create balls of dough, placing a Junior Mint into the center of each ball. Space balls of dough evenly on the pan, at least 2 inches apart.
Bake for 10 to 11 minutes. Remove pans from oven and allow cookies to sit on pans for 2 minutes before transferring to wire racks to cool completely.
Notes
Flour - If you'd rather not use whole wheat flour, substitute an equal amount of all-purpose flour.
Shortening - If you'd rather not use shortening, substitute an equal amount of butter or coconut oil, but be aware that the consistency of the cookies will not be the same. They will spread more if all butter is used.