Cook the kielbasa in the olive oil in a large heavy soup pot over high heat until golden brown, 5 to 6 minutes. Add the onions, salt, pepper, and bay leaves and cook, stirring, until the onions are slightly caramelized, 12 to 15 minutes. Add the garlic and cook, stirring, until fragrant, about 1 minute. Sprinkle the flour over the onions and cook, stirring constantly, for 2 minutes. Gradually whisk in the stock and beer. Add the thyme and bring to a boil. Reduce the heat to medium-low and simmer, uncovered, stirring occasionally, for 1 hour. Add the cheese, a little at a time, stirring until nearly melted after each addition. Remove from heat, taste, and adjust seasonings if necessary. Ladle the soup into bowls and garnish with Cheesy Popcorn and minced fresh chives. To prepare the Cheesy Popcorn: In a large partially covered saucepan, heat the olive oil and 1 kernel of popcorn until hot enough to make the corn pop. Add the remaining popcorn and cook, partially covered, shaking until all the corn is popped. Transfer to a large mixing bowl and toss with the remaining ingredients until evenly coated.