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Preheat the oven to 300 degrees F (Very important.)
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In a cast iron frying an over medium heat, crisp cook the bacon and set it aside. Leave the fat in the pan.
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Cut the beef roast in small cubes, 3/4 to an inch.
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Season the beef cubes with salt and pepper and toss in the flour until all of the flour has coated the beef.
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Brown the beef cubes in the bacon fat over medium high heat.
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Share the beef cubes and crisp bacon evenly among 6 meal mugs.
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Drain off the excess fat from the cast iron pan and deglaze the pan with the red wine. To do this return the pan to the stove over medium heat, add the red wine and using a wooden scraper or egg turner, scrape all of the flavourful bits off the bottom of the pan and into the red wine..
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Share the deglazed pan contents evenly among the 6 meal mugs.
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Share the carrots, onions and garlic among the 6 meal mugs.
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Add 1/2 a bay leaf to each meal mug.
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Add a pinch of salt and pepper to each mug along with a pinch of nutmeg and thyme. Give the contents of the mug a good stir to combine.
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At this point you can add extra carrots and onions to fill the mugs to about 3/4 full if they are not already.
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Top the mugs up to just under 3/4 full with the beef stock. It is ok to add extra beef stock during the cooking time if need be. It will reduce in the cooking time.
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Cover the tops of the meal mug tightly with aluminum foil. Place the mugs on a cookie sheet and place in the oven for about 2 1/2 hours.
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Check on the contents of the cups every hour or so and add additional beef stock if necessary.
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In the last hour or so of cooking add the mushrooms to the cups.
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The Bourguignonne is cooked when the beef is fall apart tender.
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Remove from the oven, remove the foil and let the mugs cool for 15 minutes or so.
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Increase the heat to 400 degrees F while the mugs are cooling off a little.
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To finish the pot pies, brush a little egg wash around the mugs and place a square of puff pastry over each. Quickly get them back into the oven and let them bake for an additional 15 minutes or until the pastry is golden brown. (See alternative make-ahead method in notes.)
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Serve immediately.