Step 1: Place fresh unshelled clams in a large, heavy Dutch oven, and add about 4 cups water, then set over medium-high heat. Cover, and cook until clams have opened, approximately 10 to 15 minutes. (Clams that fail to open after 15 to 20 minutes should be discarded.) Strain clam broth through a sieve lined with cheesecloth or doubled-up paper towels, and set aside the hot broth aside. Remove clams from shells, and set clam meat aside as well. Discard clam shells.
Step 2: Rinse out the Dutch oven and return it to stove. Add butter to Dutch oven, and turn heat to medium-low. Add bacon and cook about 4 to 7 minutes, stirring occasionally, until the fat has rendered and the pork has started to brown. Use a slotted spoon to remove pork from fat, and set aside.
Step 3: Add onions, garlic, celery, green peppers and carrots to the fat, and cook about 10 to 15 minutes, stirring frequently, or until the vegetables are soft but not brown. Season as desired with red pepper flakes (use sparingly, as the heat increases a bit over time.) Stir in diced potatoes, and continue cooking 5 to 7 minutes longer or until potatoes have just started to soften. Add 4 to 4 1/2 cups of reserved clam broth (save the remaining clam broth for another use). Add sprigs of thyme and the bay leaf to the brothy mixture.
Step 4: Partly cover the pot, and simmer gently until potatoes are tender, approximately 10 to 15 minutes. Using the back of a wooden spoon, smash a few potatoes against the side of the pot to release their starch and help thicken the broth.
Step 5: Meanwhile, chop the clams into bits that are about the size of the diced bacon.
Step 6: When potatoes are tender, stir in tomatoes, and heat them through (about 2 to 3 minutes longer). Add chopped clams and reserved bacon, stirring to combine. Add black pepper to taste. Let chowder come to a simmer, and remove from heat. Remove thyme sprigs and the bay leaf, and discard.
Step 7: The chowder should be allowed to cool and sit at least 3 to 4 hours to cure (allowing the flavor to mature and improve). Reheat it before serving. Garnish servings with chopped parsley. Serve with oyster crackers (if using), and serve immediately while still hot.
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