Heat oil in large, heavy stockpot on medium. Add onions and 11/2 teaspoons salt, reduce heat to low and cook, stirring occasionally, until onions are tender and have released their liquid, 10 minutes.  Increase heat to medium-high and continue cooking, stirring often and scraping bottom of pot, until onions are deep brown and caramelized, 40 to 50 minutes. If bottom of pot starts to get too dark, add 4 to 5 tablespoons water.  Sprinkle onions with flour and cook, stirring, 2 minutes. Stir in cognac and cook 1 minute. Add broth and herbs and simmer until reduced to about 8 cups, 18 to 20 minutes. Discard herbs and stir in vinegar. When ready to serve, heat broiler. Arrange bread on rimmed baking sheet and sprinkle with cheese and some fresh thyme leaves. Broil in top third of oven until golden brown and bubbling, about 1 minute. Serve on top of soup.