Step 1The night before cooking, combine the ground coffee, salt, sugar and chipotle flakes. Spread over both sides of the brisket. Cover and refrigerate overnight.
Step 2Heat the oven to 350 degrees.
Step 3Spread the onions, carrots and thyme into a roasting pan just large enough to hold the meat. Rinse the coating off the brisket and lay it on top of the vegetables, fattier side up. Pour the stock and coffee around the meat. Cover tightly with a lid or with foil and bake 3 1/2 to 4 hours, until the meat is very tender.
Step 4Remove the meat from the juices and place on a rimmed carving board. Using a slotted spoon, remove the vegetables to a bowl. Pour the warm pan juices into a gravy separator.
Step 5To serve, slice the meat across the grain into very thin slices. Spoon some of the vegetables alongside. Season the warm defatted pan juices to taste and serve on the side.