In a medium bowl, whisk together all-purpose flour, whole wheat flour, cinnamon, kosher salt, baking powder, and baking soda.

In a large bowl, mix brown sugar, melted butter, and granulated sugar. Stir in eggs, then add vanilla. Stir in dry ingredients until just combined. Fold in chocolate chips.

Scoop out 12 (1/3-cup) portions of dough (about 100 g). Roll each into a ball and arrange on a parchment-lined baking sheet. Refrigerate until cold, about 10 minutes.

Take a portion of dough and flatten into a 4" circle in your palm. Place one graham cracker square in the center, top with a piece of chocolate, a marshmallow, and a second graham cracker. Enclose dough around the filling and place back on the baking sheet. Repeat with the remaining dough, graham crackers, and marshmallows. Freeze until very firm, 30 to 35 minutes.

Preheat your oven to 375?F (190?C) and place a rack in the center. Divide the dough between two parchment-lined baking sheets, spacing them 3 inches apart. Sprinkle the tops with flaky sea salt.

Bake the cookies, rotating the sheets halfway through, until lightly browned around the edges and just set on top, about 16 to 18 minutes.

Let the cookies cool for 5 minutes on the baking sheet, before transferring them to a wire rack to cool completely.