Heat olive oil in a pan over medium high heat until it is almost to the smoking point. Add the shallots, onions, and garlic. Stir and cook until it starts to brown. Then, turn down the heat and continue cooking until it becomes soft.
Turn the heat back up to high. Then add the cognac. Burn off the alcohol and reduce until the liquid is just a coating. Then stir in the agave and cook until the whole thing begins to thicken.
Turn off the heat and add the chives and thyme. Season with salt and pepper. Then transfer to a container and refrigerate. It will have a jam like consistency when cooled. Use this on a variety of dishes, Pizzas, sandwiches, or as a condiment on appetizers or entrees.