Place pie pastry into glass or ceramic 9" pie plate. Press bottom and sides into plate and finish the edges of the crust by pressing the tines of a fork against the rim or by pursing the edges together between your thumb and forefinger. Refrigerate crust until oven has heated completely. Place pie plate into the oven and bake for 6-7 minutes until crust is set and just starting to brown. Remove crust from oven and set aside.
Reduce oven temperature to 325 degrees.
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.
While the onions reduce, in a large bowl combine the eggs, milk, cream, black pepper and nutmeg. 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.
Place a piece of aluminum foil on an edged baking sheet. Set the pie shell on top of the foil.
Pour the egg mixture into the prepared pie shell.
Cut a piece of foil about 10" square.
Place the baking sheet into the oven and carefully set the foil on top of the pie crust (not touching the egg mixture. (this will prevent over browning the crust). Bake for 30 minutes. Remove the foil and continue baking for 15 minutes, until quiche is set.
Notes
Reheat leftovers in a low 300°-325° F oven for 10-15 minutes.