1. Toss the cherries, sugar and almond extract together in a medium bowl and let stand at least 2 hours. Drain the cherries, reserving 1/2 cup of the juice.
2. Set a rack in the center of the oven and heat the oven to 325 degrees F. Butter and flour a 13 x 9 x 2-inch metal baking pan.
3. In a medium bowl, whisk the boiling water and cocoa until smooth. Whisk in the reserved 1/2 cup of cherry juices and vanilla. Let cool to tepid.
4. In a separate medium bowl, whisk the flour, baking soda, and salt until well combined.
5. In a large or medium bowl, beat the butter and brown sugar with a mixer at moderately high speed until pale and fluffy, about 5 minutes.
6. Add the eggs, one at a time, beating 30 seconds after each. (The mixture may appear curdly after the fourth egg is added, don't worry about it.)
7. Turn the mixer down to slow speed. Add the flour mixture and cocoa mixture alternately in three batches each, beginning with the flour mixture and blending each batch thoroughly before adding the next.
8. Stop the mixer, scrape the sides of the bowl with a rubber spatula, and beat at slow speed 10 seconds longer. Stir in the cherries and chocolate chips.
9. Pour the batter into the prepared pan and smooth the top.
10. Bake until a wooden pick inserted in the center comes out clean, 35 to 45 minutes.
11. Place the pan on a rack and cool the cake completely in the pan.
12. Cut into squares and dust with confectioner's sugar just before serving