Chocolate Thumbprint Cookies

For the Cookies:
2 cups all-purpose flour
1 cup plus 1 tablespoon unsweetened Dutch-process cocoa powder
2 teaspoons coarse salt
8 ounces (2 sticks) unsalted butter, softened
1 1/3 cups sugar, plus more for rolling
2 large egg yolks
2 T heavy cream
2 teaspoons pure vanilla extract
Chocolate and Vanilla-Bean Ganache (recipe follows)

For the Chocolate and Vanilla-Bean Ganache:
1/3 cup honey
1/3 cup heavy cream
1/2 vanilla bean, split and scraped, pod reserved
4 ounces bittersweet chocolate (preferably 61% cacao), finely chopped
1 ounce (2 T) unsalted butter, cut into pieces and softened

To prepare the cookies:
Preheat oven to 350 degrees. Sift flour, cocoa powder, and salt into a small bowl. Cream butter and sugar with a mixer until pale and fluffy. Reduce speed to medium, add yolks, cream, and vanilla. Scrape sides of bowl. Beat in flour mixture until just combined.

Roll balls using 2 teaspoons dough for each, and roll each in sugar. Place 1 inch apart on parchment-lined baking sheets. With the handle of a wooden spoon, press gently in the center of each to create an indentation. Bake, rotating sheets halfway through, until cookies are just set, about 10 minutes. (If indentations lose definition, press centers again.) Let cool slightly on baking sheets. Transfer cookies to wire racks, and let cool.

Spoon warm ganache into center of each cookie. Let stand until firm, about 15 minutes. Cookies will keep, covered, for up to 3 days.

To prepare the ganache:
Combine honey, cream, and vanilla seeds and pod in a medium saucepan over medium heat. Bring to a simmer and cook, stirring until honey dissolves. Remove from heat, cover, and let stand for 20 minutes.

Place chocolate in a food processor. Return cream mixture to a simmer then strain through a fine sieve. Discard solids. Pour cream mixture over chocolate, and let stand for 1 minute. Process until smooth. Add butter, and continue to process, scraping down sides occasionally, until butter is incorporated. Let cool slightly, and then use immediately.