To make the vanilla layer, whisk together the flour and salt together in a medium bowl. In the bowl of a stand mixer fitted with the paddle attachment, cream the butter and sugar together on medium speed until light and fluffy, about 3 minutes.
Add the vanilla, agave, and eggs and mix until combined, scraping down the bowl as needed. Mix in the dry ingredients until combined and no flour shows. Do not overmix. The dough will be a little sticky.
Transfer the dough to a lightly floured surface and divide it in half. Roll each piece of dough into a 6-inch log about 2 inches thick. Wrap each section of dough tightly in plastic wrap and refrigerate until firm, about 1 to 1 1/2 hours.
To make the chocolate layer, whisk the flour, cocoa powder and salt together in a medium bowl; set aside.
In the bowl of a stand mixer fitted with the paddle attachment, cream the butter and sugar together on medium speed until light and fluffy, about 3 minutes. Add the vanilla and eggs and mix until combined, scraping down the side of the bowl as needed.
Add the flour mixture and mix on low speed until the flour no longer shows. Be sure no to overmix. The dough will be a little sticky.
Transfer the dough to a lightly floured surface and divide it in half. Roll each piece of dough into a 6-inch log about 2 inches thick. Wrap the dough tightly in plastic wrap and refrigerate until firm, about 1 to 1 1/2 hours.
To make the cookies, preheat oven to 350° F and line a baking sheet with parchment paper.
One a lightly floured surface, roll one vanilla dough log into a 9x11-inch rectangle. Repeat with one chocolate dough log. Flip the chocolate dough on top of the vanilla dough so that the chocolate dough is layered on top of the vanilla dough. Lightly flour a rolling pin and gently roll over the top with a rolling pin to make the doughs stick to one another. Roll up the dough into one big log, pressing gently as you roll to adhere the dough. Wrap the rolled dough and place in the refrigerator for 1 to 2 hours or until firm. This will make it easier to slice.
Carefully slice the log into 1/4-inch-thick cookies. Repeat with the remaining two dough logs. Bake 10 to 12 minutes, or until the cookies are no longer shiny and the edges are just starting to brown. Do not overbake, this will keep the cookies nice and soft.
When the cookies come out of the oven and while they are still hot, I like to use a small spatula to round the edges so that they all look uniform.
Let cook on the baking sheet for 2 minutes, then transfer to a wire cooling rack.