As the onions and mushrooms are cooking and the pasta water is coming to a boil, we place the butter into a pot and begin melting it over low heat.
The pasta water has come to a boil so we add some salt and the pasta. We stir and time the pasta for a couple of minutes shy of the package directions. We will keep checking the pasta to see when it is al dente.
As soon as the pasta goes in the pot, we see that the mushrooms have released their liquid and are browning, so we add the chopped yellow squash, broccoli and garlic. We stir and add the fresh thyme sprigs and some salt and pepper. The stock is added, the heat lowered to medium-low, and the pot partially covered.
The butter has melted in our pot and we add the flour. We stir with our “roux whisk” (a flat whisk – but a wooden spoon and regular whisk would work) and cook over medium-low heat for 2 minutes. Meanwhile, we place the milk in the microwave for 1 minute to heat. When the flour-butter mixture has cooked for 2 minutes, we add the milk and whisk to remove all lumps. We raise the heat slightly and bring the mixture to a boil. We lower the heat and simmer gently for a couple of minutes.
We zest the lemon half into the white sauce, and squeeze the lemon (straining the seeds) in as well. Lastly, we add the cheese, stir, and set aside.
When the pasta is cooked, we drain it in a colander. We pour the lemon sauce into the simmering vegetables and add most of the cooked pasta (we reserve some for the children). We add the chopped tomatoes and tear in the fresh basil. The pasta is tasted for salt and pepper and re-seasoned. We serve topped with red pepper flakes and more cheese.