Finely slice the onions and add to a large saucepan with the butter, bay leaves, thyme and a pinch of salt. Cook over a medium-low heat, stirring every few minutes to make sure it doesn’t stick, for about 20-25 minutes until golden.
Add the flour, mix well, then add the brandy and bubble down. Add the stock and bring to a simmer, stirring often, for 5 minutes. Taste, and add more seasoning if necessary.
For the croutons, put the grill on high, the drizzle the olive oil onto a baking tray, then rub the bread in the oil to ensure an even coating. Put under the grill for 3-4 minutes until beginning to turn toast, then pile on the grated cheese. Put back under the grill and cook until the cheese is bubbling and golden.