I have the same problem with my clutch pedal when weather gets wet
This issue arises when one attempts to pivot the foot on its heel when pressing the clutch pedal (at least at the very beginning of the entire pressing motion). Apparently, according to the opinion of some drivers on the net, this is not the right way to do it. The foot is not supposed to be pivoted on the heel. Instead the clutch pedal should be pressed by straightening the entire leg, with the heel floating and sliding forward above the floor. When you do it that way, the shoe sole does not slide over the clutch pedal and does not make that terrible sound.
It works too, but I still stick to the habit of resting the left foot on the heel and pivoting it when pressing the clutch pedal.