Use a sharp knife to slice beef chuck into 1 1/2-2" pieces. Pat beef with a paper towel to dry, then season liberally with salt and black pepper. Heat olive oil in a heavy bottomed pot (I love to use my dutch oven) over HIGH heat.
Add beef, in a single layer, to the pot and brown on all sides. Be careful, as the oil may spatter. Remove browned beef to a plate, then repeat with remaining beef.
Lower heat to MED, then add chopped onions and garlic. Season with salt, and cook until softened, about 3-4 minutes.
Add bacon pieces and cook until browned. Add flour and stir to combine well. Let floured mixture cook 1 minute to remove any raw flour taste.
Pour in Guinness beer and stir well to combine and loosen any browned bits from the bottom of the pot. Add tomato paste, chicken stock, carrots, celery, parsnip, bay leaves, thyme and coffee.
Return beef to the pot and stir. If needed, add enough water so that the beef and veggies are nearly fully covered.
Bring to a bubble, then reduce heat to LOW or so that it's simmering, cover, and simmer for 2 hours.
Remove lid, add potatoes and chopped prunes, stir, then simmer UNcovered another 30-40 minutes, until sauce has thickened to a loose gravy consistency, beef is incredibly tender and potatoes are fork tender.
If needed, skim residual fat off the surface. Taste, and adjust salt and pepper as needed. Remove bay leaves and serve.