Preheat oven to 250 degrees. Pat beef dry, cut into large cubes, and season with salt and pepper. Divide flour and beef between 2 (1-quart) sealable plastic bags, seal, then shake to coat meat.
Heat 1‚ tablespoons oil and 1 1/2 tablespoons butter in a wide 6- to 8-quart heavy Dutch oven over moderately high heat until hot but not smoking, then brown beef well on all sides in 2 or 3 batches, without crowding, adding remaining tablespoon oil as needed. Transfer to a bowl.
Pour off any excess oil from pot, then add brandy to pot. Deglaze by boiling over high heat 1 minute, stirring and scraping up brown bits, then pour over beef.
Heat 1 tablespoon butter in cleaned pot over moderately high heat until foam subsides, then sauté bacon, stirring, 2 minutes. Add chopped onions, celery, garlic, and carrots, then sauté, stirring, until onions are pale golden, about 5 minutes. Add tomato paste and cook, stirring, 1 minute. Add wine, meat with juices, all the herbs and simmer gently, partially covered, until meat is tender, 3 1/2 to 4 hours.
While meat simmers, blanch boiling onions in boiling salted water 1 minute and drain in a colander. Rinse under cold running water.
Heat 1 tablespoon butter in a 3-quart heavy saucepan over moderately high heat until foam subsides, then saute boiling onions, stirring occasionally, until browned in patches. Season with salt and pepper. Add 2 cups water (1 1/2 cups if using pearl onions), then simmer, partially covered, until onions are tender, 15 to 20 minutes. Boil, uncovered, stirring occasionally, until liquid is reduced to a glaze, 5 to 10 minutes.
Heat remaining tablespoon butter in a large nonstick skillet over moderately high heat until foam subsides, then saute mushrooms, stirring, until golden brown and any liquid mushrooms give off is evaporated, about 8 minutes. Season with salt and pepper.
Stir onions and mushrooms into stew and cook 10 minutes. Remove bay leaves and skim any fat from surface of stew. Season with salt and pepper.