Add all of the raspberry filling ingredients to a medium saucepan set over low/medium heat. Cook for 25-30 minutes, stirring occasionally. Once the raspberries have thickened to create a jam, remove the pan from the heat and let the filling cool.
While the raspberry filling is cooking, make the cookie dough. In a medium bowl, mix the almond flour, baking soda, and salt together. In another medium bowl, use a spatula (or hand mixer with beaters) to mix the egg, vanilla, honey, and room temperature butter together.
Slowly add the dry ingredients to the wet ingredients and mix until combined.
Shape the dough into a ball, wrap in parchment paper or plastic wrap, and refrigerate for 30 minutes.
While the dough chills, preheat the oven to 350ºF. Line a baking sheet with parchment paper. Set aside.
Once chilled, remove the dough from the refrigerator. Use a tablespoon scoop to roll the cookie dough into balls and place them 2 inches apart on the prepared baking sheet. Use your thumb to press in the middle of each cookie dough ball to create a "thumbprint." Repeat.
Bake for 9-11 minutes until the edges are slightly golden brown.
Remove the cookies from the oven and carefully re-indent the middle of each cookie with a teaspoon or handle end of a wooden spatula.
Once the cookies are completely cool,* fill the middle of each cookie with 1-2 teaspoons of the raspberry filling.