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Cut the onions in half lengthways, then slice down into very thin slices. Heat a very large pan, add the oil when hot, stir in the onions, 3 of the thyme sprigs and the bay leaves, then season with a little salt. It will seem like a lot of onions, but they reduce right down. Cook over a high heat for 5 mins, stirring often. The onions shouldn’t brown yet, just start to soften. Lower the heat, then cook slowly for 35 mins, uncovered, stirring often until the onions have reduced right down and are very soft.
While the onions are cooking, bring the wine to a boil in a small pan, then bubble away for 30 secs. Remove and leave to cool. Tip the flour into a small heavy pan and toast over a medium heat for a few mins, stirring occasionally, until light brown in colour. Set aside.
When the onions are very soft and reduced, turn up the heat so they caramelise, then cook for another 12-15 mins, stirring along the bottom of the pan occasionally to mix in the brown sticky bits. When the bottom of the pan and all the onions are sticky and a rich brown colour, stir in the flour. With the heat still high, gradually pour in the wine, again stirring in the bits from the bottom. Pour in 1.2 litres of cold water. Stir in the bouillon, then slowly bring everything to the boil. Skim off any froth from the surface. Simmer for 15 mins so all the flavours can mingle.
While the soup simmers, make the topping. Heat oven to 200C/fan 180C/gas 6. Mix the garlic and the oil together. Brush all over the bread slices, then cut each one into cubes. Scatter over a baking sheet, then bake for 8-10 mins until golden. Set aside. Line a baking sheet with baking parchment or a sheet of non-stick silicone. Remove the leaves from the remaining thyme sprig, then mix with the grated Parmesan. Scatter and spread over the lined baking sheet into a 13 x 8cm rectangle. Bake for about 8 mins until melted and turning golden. Remove, leave to firm up, then snap into jagged pieces.
To serve, remove and discard the herbs from the soup. Ladle the soup into bowls – scatter over a few croutons, the gruyère and a grinding of pepper, then perch a parmesan crisp on top. Serve any remaining croutons separately.