In a medium bowl, whisk together the flour, baking soda, cinnamon, salt, and nutmeg, if using. Set aside.
In the bowl of a stand mixer, add the butter, brown sugar, and granulated sugar. Beat with the paddle attachment until creamy and smooth, scraping down the sides with a spatula if necessary. This should take 1 to 2 minutes.
Add in the egg, egg yolk, and vanilla extract and beat until combined and smooth.
With the mixer off, add all of the dry ingredients. Turn the mixer on low and mix until just combined. Stir in the oats.
Line large baking sheets with a Silpat baking mat or parchment paper. Scoop the cookie dough into round balls, about 2 tablespoons per ball. Place on the lined baking sheets, about 2-inches apart. Bake for 10 to 12 minutes or until the edges of the cookies are golden brown but the centers are still light golden and soft. Remove from the oven and sprinkle the cookies with flaked sea salt. Let the cookies cool on the baking sheet for 5 minutes. Transfer cookies to a wire cooling rack to cool completely.