In a large saucepan, heat 2 tablespoons olive oil over medium to medium low heat. Add sliced onions and sprinkle with the salt. Stir and cover. Let the onions caramelize in the pot, stirring occasionally. This may take 40-45 minutes. You don't have to hover over the pot, just check on it every 7-8 minutes and stir, adjusting heat if too hot or cool. You want the onions to slump after they've given off their liquid, then begin to caramelize and brown slightly.
Preheat oven to 220 degrees. Grease muffin tin and line the muffin holes with the puff pastry squares, pressing into the edges of the shape.
Refrigerate crust until oven has heated completely. Place tray into the oven and bake for 5 minutes until crust is set and just starting to brown. Remove crust from oven and set aside.
Reduce oven temperature to 160 degrees. While the onions cool down, in a large bowl combine the eggs, milk, cream, black pepper and salt. Whisk to combine.
Add the cheese to the egg mixture and stir.
When the onions have finished caramelizing, add the thyme to them and stir well.
Take a spoonful of the onions and add them to the egg mixture, stirring well. Continue to add the onions to the eggs a spoonful at a time, to temper the egg mixture.
Pour the egg mixture into the pie shapes. Place the baking sheet into the oven and bake for 25 minutes.
As soon as they come out of the oven, top with a slice of brie and teaspoon of cranberry sauce.
