Bring a large pot of water to a boil. Lightly salt the boiling water, and add in the linguine pasta. Cook until just halfway through the cooking time suggested on the package. Remove ¼ cup (60 ml) of pasta cooking water from the pot, and set it aside.
Heat the extra-virgin olive oil in a large pan over medium-high heat. Add in the garlic and chili (if using) and a sprinkle of lemon zest, followed by the clams, and sauté all the ingredients for 2 minutes, then sprinkle them with fresh chopped parsley and/or lemon thyme.
Cover the pot with a lid and simmer until the clams open, about 2 minutes. Discard the garlic clove and the clams that did not open, then pour the clam sauce through a sieve or cheesecloth, and set it aside.
Drain the linguine pasta, and add it to the pan with the clams. Pour in the reserved filtered clam sauce and continue cooking the pasta, adding a ladle of reserved pasta water at a time, until the linguine are al dente.
Remove the pan from the heat, sprinkle with the lemon zest and the remaining thyme leaves and parsley, and toss gently to combine all the ingredients.
Serve immediately with freshly-cracked black pepper on top.