Melt butter in a saucepan over medium-high heat, then whisk in flour to make a roux. Lee likes to cook it until it gets a little bit brown. Put roux aside to let cool. In a large stockpot (16-quart), cook bacon until very lightly browned. Add onion and thyme to the pot, and sauté until lightly translucent. Add celery to the pot and stir. Add juice, including juice from the chopped clams, along with clam base and bay leaves to the pot. Bring to a boil, then add potatoes, and let them cook until a little tender. Add room-temperature roux a little bit at a time until thickened. Add cream, garlic, and black pepper, return to a light boil, and add chopped clams. Remove from heat and adjust the seasonings if needed.