Preparation

• In a large saucepot, saute the bacon over medium-high heat until the fat is rendered and the bacon is crisp, about 10 minutes. Remove the bacon with a slotted spoon, place on a paper towel-lined plate and set aside.
• Lower the heat to medium and sweat the celery, leek and shallot in the bacon fat until soft, about 6 minutes. Add the garlic and sweat until fragrant, 1 to 2 minutes. Do not brown the vegetables. Remove the pot from the heat and set aside.
• In a separate saucepot over low heat, warm the roux. Add ½ cup clam stock and whisk until the liquid is incorporated, then add another ½ cup stock. Whisk another 1 cup stock into the roux until incorporated.
• Pour the remaining 2 cups stock into the saucepot with the vegetables over low heat, then add the roux and whisk until everything is incorporated. Add the potatoes, thyme sprigs and bay leaf and stir to coat. Raise the heat to medium and let simmer, stirring often, until the potatoes are barely fork-tender, about 15 minutes. The mixture will look thick and gluey.
• Remove the saucepot from the heat and slowly stir in 2 cups milk until combined. Fold in the littleneck and quahog clam meat and the bacon and season to taste with salt and pepper. Let the chowder cool completely and refrigerate overnight to let the flavors intensify.
• Before serving, place the pot of cold chowder over medium-low heat, stirring occasionally until warmed through. Add the remaining ½ cup milk and stir to combine, adding more milk to thin if desired. Remove and discard the bay leaf and thyme sprigs. Season with salt and pepper. Garnish with chives and serve with oyster crackers.