Next, in the same pan, add the yellow onions and sauté over medium heat, until they are past transparent. Add leeks, shallots, garlic and season with salt. Continue to cook, until the mixture has a nice dark brown (not burnt) color are sweet aroma. At the middle to end of cooking, start adding 2/3’s of the herbs, reserving the last 1/3 for the finishing of the soup. As the mixture finishes it’s caramelization, deglaze the pan with 3/4 of the bottle of Imperial Red Ale, about 16 ounces. Stir the bottom of the pan to remove any browned bits. Pour mixture in with other vegetables. Add stones (does add a nice mineral component to the soup), bay leaves and stock/water. Bring to a simmer and cook for about 20-30 minutes or until all the vegetables are cooked through, but not overcooked into a mush. Test for salt and pepper, adding the remaining herbs and beer, to re-freshen the flavors.