This recipe is adapted from Cook's Illustrated Holiday Baking magazine. I love to add orange blossom water to the cookies; all-vanillais good too. To make-ahead and freeze the cookies, after indenting the unbaked thumbprints, freeze them on cookie sheets, then place in freezer bags. Bake from frozen (don't thaw) for about 15 minutes, then reshape the indentations with the back of a teaspoon and proceed with the recipe as usual from there.
Preheat oven to 350°F. Line 2 large baking sheets with parchment paper. In a medium bowl, whisk the flour, salt, baking soda, and baking powder.
Beat the butter and sugar on medium speed until the mixture is light and fluffy, 3 to 6 minutes. Beat in the cream cheese, egg, flowerwater, and vanilla until combined, about 30 seconds, scraping down the sides of the bowl as needed.
Reduce mixer to low and slowly add the flour mixture just until combined.
Roll the dough into balls between the palms of your hands, about 1 ½ teaspoons of dough per ball. Place them on the prepared baking sheets about 1 ½ inches apart. Use your thumb, moistened in water to prevent sticking, to indent the center of each cookie.
Bake until the cookies are just beginning to set, about 10 minutes. Remove the pan from the oven and, working quickly, reshape the indentation using the rounded bottom of a teaspoon. Use a small spoon to carefully fill the indentations with jam.
Return the cookies to the oven and bake until light golden,12 to 14 minutes.
Cool the cookies for 10 minutes on the sheets, then transfer to a wire rack to cool completely before serving.