Fill a large pot or dutch oven half full of water. Add one tablespoon of salt to the water and bring to a boil over medium-high heat.
Cook the pasta per the package directions for al dente pasta.
Before draining the pasta, remove 1 cup of the pasta water with a measuring cup and set aside.
Using the same large pot or dutch oven, add the olive oil and heat on medium heat. Then add the minced shallots and cook for 2-3 minutes or until the shallot is translucent and tender.
Then add the garlic, thyme, and red pepper flakes and stir constantly for one minute.
Add the butter and stir continuously until it has melted.
Once butter has melted, add in the flour and stir for one minute until it gets thick and starts to turn slightly brown.
Slowly add in the milk, stirring continuously until there are no lumps. Use a whisk to help break up the lumps if necessary.
Then add the pasta water that was removed.
Cook the sauce for 3-4 minutes or until it has thickened enough to stick to the spoon slightly.
Remove the pot from the heat and add the freshly shredded cheddar cheese and ground nutmeg. Stir until the cheese has completely melted.
Then add the cooked pasta and stir to combine well.