CUT ends of onions and peel outer layers; CUT onions to 1/4-inch thick slices; HEAT 2 tablespoons unsalted butter and 1 tablespoon vegetable oil in a heavy-bottomed soup pot over medium-low heat; SAUTE onions covered for 20 minutes; ADD 1 teaspoon kosher salt and 3/4 teaspoon packed brown sugar (or 1/2 teaspoon granulated sugar); RAISE heat to medium-high and cook, stirring often, until onions caramelize and turn a rich brown; ADD two mashed garlic cloves; STIR.
REDUCE heat again to medium-low; SPRINKLE 3 tablespoons all-purpose flour over onion mixture; COOK, stirring often, for 2 minutes.
DEGLAZE the pan with the cognac and sherry, scraping bottom of SIMMER uncovered for about 5 minutes.
STIR in the dry wine; SIMMER uncovered for 15 minutes.
ADD 6 cups beef stock, 2 bay leaves, 1 fresh thyme sprig (or 1/8 teaspoon ground thyme), 1/4 teaspoon ground sage, 1/8 teaspoon fresh ground black pepper, and 1/8 teaspoon fresh ground white pepper; SIMMER uncovered for at least 30 minutes.
REMOVE bay leaves and thyme sprig; SEASON just to taste with just enough grated parmesan cheese to flavor the stock (no more than 2 tablespoons), and kosher salt, to taste.
MEANWHILE, fresh sourdough French baguette bread into slices to place across soup in serving bowls (cut to 1/2 - 3/4 inch thick, number of slices depends on size of bread/serving bowls); SHRED 6 ounces gruyere cheese.
DRIZZLE each slice bread on both sides with olive oil; BAKE bread on a baking sheet at 325 F for 15 minutes; TURN croutes over on baking sheet and continue baking 10-15 minutes, until bread is very toasty (it will be quite hard, which is what you want); REMOVE bread from oven; SET broiler to high.
LADLE soup into four bowls; PLACE croutes into each bowl; COVER each croute completely to the rim of bowls with shredded gruyere cheese (about 1/3 cup for each).
PLACE bowls on a baking sheet under broiler just until cheese melts and begins to brown (keep an eye on them, about 45 seconds to 1 1/2 minutes); REMOVE from oven; SPRINKLE each lightly with grated fresh parmesan cheese and fresh snipped chives if desired; SERVE and enjoy!