Pat the chicken thighs dry with a paper towel. Season with the salt and pepper. Set aside.
In an ovenproof skillet, heat the olive oil over medium-high heat. When hot, add chicken thighs, browning well on both sides, approximately 4 minutes on each side. They will not be fully cooked. Remove to a plate and set aside.
In the same pan, without wiping, add cut bacon. Cook until browned and crispy. Remove using a slotted spoon, reserving bacon fat in the pan.
Reduce heat to medium and add the shallots to the hot skillet. Caramelize, turning over so often for 15-20 minutes or until the exteriors are browned and soft.
Add the chicken back to the pan and deglaze with white wine. Add the Dijon mustard and tarragon, stirring into the sauce as best you can.
Cover with a lid or a sheet of aluminum foil and transfer to hot oven. Braise for 30 minutes or until chicken registrars at 165°F.
When about to remove, stir together the melted butter and flour to make a paste.
Remove skillet from the oven and return to the stove over low heat. Dollop the butter paste into the sauce, using a fork to whisk in the little pockets. Sauce will start to thicken. Spoon over chicken and shallots.
Add the tomatoes, tossing with sauce as well. Heat for 3-4 minutes allowing for the tomatoes to heat, but not actually cook.
Serve over rice or paste and garnish with the chives.
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Notes
*You can opt to use bone-in as well. ** Use 2 teaspoons of dried tarragon in place of fresh. Nutritional calculation do not include pasta or rice.