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That's bad for the clutch. It's also bad for the clutch to keep your hand rested on the shifter while you drive. I put the pedal down pretty much all the way but not touching the stopper.
Its bad for the transmission (shift forks) to rest your hand on the shifter. Has nothing to do with the the clutch.
Holding the clutch down at red lights is bad for the throw-out bearing. It will prematurely wear it out (~50,000 miles). The 10-second rule is your friend on this one. You should sit in neutral with your foot off the clutch pedal at lights.