Warm the olive oil in a skillet over medium heat. Stir in the shallots and garlic; add a pinch of salt. Cook for about 5 minutes, stirring often, or until the shallots are softened and beginning to brown.
Transfer the cooked shallots and garlic to a 5-6 quart slow cooker. Add the mushrooms, beans, broth, wine, tomato paste, and thyme and stir well. Cover and cook on low for 6 hours.
When there are 30 minutes left on the timer, open the lid and give the stew a good stir; taste and season with salt and pepper.
Top the stew with the bread cubes; press them down into the stew a bit so they soak up the broth, then sprinkle the cheese over the bread. Replace the cover and cook for the remaining 30 minutes, or until the cheese has melted, then serve.