Heat oil and add onions. Cook over medium heat for 15 to 20 minutes, until softened. Add thyme, salt and pepper. Cook for 2 minutes, remove from heat and allow to cool.
Preheat oven to 425 degrees. Place puff pastry shells on baking sheet and bake for 15 minutes. Remove lid and fill with onion mixture. Top with goat cheese. Bake for 5 minutes until golden brown. Let cool before serving.
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