Bring a large pot of water to a rolling boil, add a generous pinch of salt, and cook the linguine until it is about halfway done according to the package directions. Reserve 1/4 cup (60 ml) of the pasta cooking water, then drain the pasta and set aside.
Meanwhile, heat the extra-virgin olive oil in a large skillet over medium-high heat. Add the garlic (whole clove or minced as preferred) and the minced red chili if using, plus a little lemon zest, and sauté briefly until fragrant, about 30 seconds to 1 minute.
Add the cleaned clams to the pan and sprinkle with half of the chopped thyme/parsley. Sauté the clams with the aromatics for about 2 minutes.
Cover the skillet and cook until most clams have opened, about 2 minutes; discard any clams that remain closed. Remove and discard the whole garlic clove if used.
Pour the pan juices through a fine sieve or cheesecloth into a bowl to remove any grit and set the strained clam liquid aside.
Return the skillet with the clams to medium heat, add the partially cooked linguine, and pour in the reserved strained clam liquid. Toss and add reserved pasta water a ladleful at a time as needed to create a silky sauce and finish cooking the pasta until al dente.
Remove from heat, sprinkle with the remaining lemon zest and chopped thyme/parsley, season with sea salt and freshly cracked black pepper to taste, and toss gently to combine.
Serve immediately while hot.
