Heat a heavy bottomed medium pot or deep skillet over medium heat. Melt butter in pot and add onions, raising heat slightly. Add bay, thyme, salt and pepper to onions and cook, stirring occasionally, until onions are soft and caramel in color, 20 minutes.
While onions cook, slice apples and douse with a little lemon juice to slow browning. Arrange the apples and bread on a board or platter.
When onions are soft and sweet, add flour and cook a minute. Whisk in wine, cook a minute then whisk in half-and-half. When the liquid comes up to a bubble, season with nutmeg and cloves and adjust salt and pepper, to taste. Stir in Cheddar and melt then remove from heat and serve in fondue pot or transfer to a small, warmed sauce pot which you can return to the stove top to reheat sauce as necessary. Dip apples and bread in warm cheesy sauce and enjoy.