Hello. I am a first time user. I have recently purchased a 2008 green jeep liberty with a sky slider and 6 speed manual. I love this machine. It looks great! I was weary of purchasing a vehicle with 100,000 mile on the odometer but it is flawless inside and out. (I swear it looks like someone towed this vehicle behind and RV it's whole life). When I test drove it you literally could only hear the noise of the tires on the road. The other day I let the clutch out with the e-brake on and I am noticing a slight chatter at idle and am concerned I may have damaged the engine slightly. Not sure how concerned I should be. Also now that I am more familiar with the vehicle I am noticing the transmission kind of clunks when I go to put it in first. Are these fairly normal conditions or should I be concerned about wear leading to other damage? I also am not sure what was done at the dealership for maintenance at 100,000 miles. They say everything.... Whatever that means. I just want to do right by the vehicle.

The 3.7L is not known to be a quiet sounding vehicle. Switch to synthetic engine oil if you haven't already. That's quieted mine down a little.
As for the transmission, not many members here have the 6 speed, I can only think of one.
Someone with a manual KJ might be able to help you out.

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2008 Black Jeep Liberty Sport
4.7L throttle body
Old Man Emu lift
Sky Slider
Hypertech Max Energy
K&N CAI
Gibson stainless steel exhaust
Blacked out
ScanGauge2
BFG All Terrrain 225/75/16
JBA upper control arms

I think I am thinking of the same one. You could try PM-ing Diggerfreek. He's got an '08 manual.

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2008 Liberty Sport 4x4 Automatic

Jeepin By Al 4" Lift Kit
BFG KO2’s 245/75R16
Full MOPAR skid plates
Rock Lizard Skink Super Sliders
AtTheHelm Front Recovery System & Roof Rack
M116A3 Trailer build thread: viewtopic.php?f=72&t=77997

I have an 08 / 6 speed as well, mine has about 68k on it. Just had the transmission / transfer case / diff oil changed at 60k.

In my experience, it does not like cold weather at all. At anything less than about 40 degrees, 1st and 2nd gear can get quite "crunchy". Letting it warm up for a minute on cold mornings definitely helps. I've noticed it sometimes shudders when pulling away from a stop when cold, but again after it warms up it's fine.