As someone who has successfully tracked calories in the past with great effort, the trick is to be strict about measuring calorie-dense foods, but to be liberal with "lighter" foods where the calories are functionally de minimis. An ounce of olive oil has 250 kilocalories. An ounce of lean protein generally has 30-50 kilocalories. An ounce of green vegetables contains virtually no kilocalories.

As such, things like oils and miso can be heavily caloric, and need to be measured strictly. This is also true of most proteins and carbs.

Seeds and tomato sauce can have some caloric density, and should also be measured, but it is less of a priority.

Mustard, lemon juice, most spices (that don't contain sugar), onions, cucumbers (regardless of density) and parsley do not have any substantial caloric density and can be considered "free" unless used in great quantities. Nobody ever gained weight from mustard, lemons, onions, cucumbers and parsley.

As already mentioned, micronutrients like vitamins are not functionally possible to be measured in a home kitchen. If you're concerned about any decrease in micronutrients, simply use vitamin and mineral supplements. Macros like proteins, carbs and fats, on the other hand, can generally be measured using typical cups, spoons and scales, even with leftovers.

When making a meal shared with others if you are looking to strictly track calories, it is easier to break things into macronutrients and mix them on individual plates or bowls rather than cook as a total pot. It's much easier to measure a protein (say, 4oz chicken), a carb (say, a potato), a sauce and a fat individually portioned on a plate than an arbitrary stew. (As above, low-calorie vegetables likely do not need to be measured separately unless there are added macronutrients.)