It's the master cylinder. It is a door creaking sound somewhere near the bottom of the pedal travel. The dealer diagnosed it and replaced my master cylinder 1.5 years ago. That replacement worked without creaks until 6 months ago. Today was the 3rd time I had to relube the cylinder. I gave in and used silicone spray into the cylinder. Smooth as new now. And I don't advise using lithium grease spray into the cylinder. It dries out as a solid film.
Lubing the cylinder didn't seem to work for me. When the creak was present did your clutch feel a bit strange at friction point? (mine does)
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