Place a 6 quart Dutch oven or similar sized heavy bottomed pot over medium heat and add the butter. When the butter melts add the thinly sliced onion to the pot. every five minutes or so check on the onions. Make sure they are not beginning to burn on the pot and give them a good stirring.As the time passes, the volume of the onions will begin to shrink and the onions will change in colour from white to a light golden or amber colour.
Make the soup
Add the garlic to the onions and saute for a couple of minutes before adding the wine. Let the onions cook with the wine until it has reduced by at least half.
Add the flour and stir well to coat the onions.
Add the beef stock, bay leafs and thyme then bring the pot to a boil. Reduce the heat to low and let the pot simmer for 20-30 minutes.
Make the croutons
Slice the baguette into thick slices then brush with olive oil on both sides before baking in the oven at 425ºF until golden brown.Spread out the shredded cheese over the croutons and place them back into the oven until the cheese melts.
Ladle the soup into bowls and place the cheesy croutons on top.
If you have oven safe soup bowls you can put the croutons with unmelted cheese straight into the soup and bake in the bowls until the cheese has melted.