Preheat oven to 400°F. Slice half of the baguette to have 2-3 slices per soup ramekin. Place bread slices on baking sheet and toast the bread slices until golden brown (See Note 2). Remove and allow to cool. Crumble into each soup ramekin on a baking sheet. Set aside.
In a heavy bottom soup pot or Dutch oven over medium low heat add the butter and oil to melt.
Add the sliced onions and stir. Cover with lid and cook for 15 minutes. Remove lid and turn heat to low. Cook, stirring often, another 15 minutes until onions are a dark golden brown.
Add the salt, pepper and flour and cook another minute. Carefully pour in the beef stock and wine, stirring to combine. Add thyme, simmer 5 minutes.
Ladle into prepared soup ramekins, top with the cheeses. Place in 400°F oven and bake for 15 minutes.
Remove from oven and serve with chopped chives on top and crusty French bread.
Use white or yellow onions, red are too sweet, but that is up to you.
Rub with fresh garlic and oil prior to toasting, optional.