Trim the ends from the onions, cut in half and peel the skins. Slice into 1/4" slices. (You can use a food processor with the wider slice attachment, but I prefer to do by hand with a very sharp knife . . . the time consuming part is the trimming and peeling.)
Divide the olive oil and butter into a large stock pot and a large saute pan (3 TBSP of each) and heat over medium heat until until the butter is just melted.
Divide the onions and add to the oil and butter and stir well. Cover and cook until the onions are soft and begin to become golden, stirring frequently to ensure they are not sticking to the bottom of the pans, about 5-7 minutes.
When the onions are soft and golden, add the shallots, sugar and salt and continue to cook, uncovered, until they become a deep golden brown and are very soft but still have texture, about another 4-5 minutes. Again, scrape the bottom of the pans frequently to ensure they are not burning.
Transfer the onions in the saute pan to those in the stock pot and add the garlic, rosemary, thyme & black pepper. Cook for about 2-3 minutes. At this point the onions should be a deep brown.
Add the flour and cook for 2 minutes.
Add the Worcestershire, Cognac and wine and cook for 2-3 minutes to cook off the alcohol.
Add the stocks, water and "Better than Bullion" (or cubes if you are using). Bring to a boil and then reduce to simmer. Simmer for 30 minutes with lid partially on (half on/half off), stirring occasionally to ensure the onions aren't sticking to bottom of the pot. Ladle into onion soup crocks, place a slice of sourdough bread (or baguette if you haven't been on the sourdough kick), top with grated gruyere cheese and place under broiler until the cheese just starts to melt.
Using a creme brulee torch, brown the melted cheese until it is nice and crusty.
Enjoy with a nice glass of red wine!