In a large stock pot, saute onions, bacon, and celery with butter for 5 to 7 minutes on medium-high heat. Add potatoes, stock, and water. Simmer on low for 30 minutes or until potatoes are almost tender. Turn down heat and slowly add cream. Whisk in flour/arrowroot. Add clams and thyme leaf, then simmer 15 to 20 minutes. Serve with crackers. Salt and pepper to taste.