1. Rinse and pat beef dry. Put beef in a shallow glass dish with marinade ingredients and chill, covered, turning occasionally, for at least 8 hours or overnight.
2. Drain beef in a sieve set over a bowl and reserve marinating liquid. Discard bouquet garni (parsley, thyme, tarragon, bay leaf, cloves, and black peppercorns, all tied together in a piece of cheesecloth) and separate beef from vegetables, reserving broth. Let beef and vegetables come to room temperature, about 20 minutes.
3. Pat beef dry and season all pieces with salt and pepper to taste.
4. Heat 3 tablespoons oil in a 6-quart heavy pot over moderately high heat until hot but not smoking and brown beef in batches, without crowding, about 5 minutes per batch, adding more oil as needed between batches. Transfer beef with a slotted spoon as browned to a bowl, reserving pot.
5. Saute mushrooms with salt and pepper to taste, stirring occasionally, until golden brown, about 3 minutes. Transfer with a slotted spoon to a bowl and reserve.
6. Stir into pot reserved marinade liquid, 1 cup water, beef, marinated vegetables, and pearl onions and bring to a boil. Reduce heat and cook at a low simmer, covered (do not boil), until meat is fork tender, about 2 hours.
7. Stir together flour and butter with a fork until combined well to create a beurre manie for thickening the stew. Stir beurre manie, mushrooms, and peas into stew. Simmer, uncovered, stirring, until slightly thickened, about 5 minutes.
8. Serve stew with boiled potatoes, if desired.