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2000 1.6 litre 5 speed manual transmission with 90,000 km that shifts very nicely when cold, but after driving for about 5 minutes and the tranny begins to warm up, the shifting becomes heavy and hard and difficult for all gears.

Played around with the clutch cable free play and changed the tranny fluid, and neither one made a difference. I can't imagine it being a worn clutch, for I baby this thing and am never hard on it. Any ideas what the problem could be? thanks.  

I have not worked on your specific vehicle but ive done a lot of clutch work .Number one im surprised that a 2000 vehicle does not have a hydraulic clutch.Anyway does it grind into reverse?How much freeplay do you have?Does the clutch pedal operate easy or hard?90,000 km not miles right.The possibilities are bad syncro rings,A bad pressure plate,bad pilot bearing{spinning the  input shaft when clutch is disengaged}or a misadjusted or stretched clutch cable.A broken or bent clutch fork .It would be unusual for all syncros to go bad at the same time unless they require special fluid and were contaminated by the wrong oil.  

It does not grind in reverse.  I've played around with the free play in the cable, and it doesn't make a difference.  The clutch pedal is fine, warm or cold.  This only happens when the tranny warms up, so something is expanding to make the shifting heavy feeling, very heavy in fact.  Btw, is there a grease nipple or something that needs lube at the base of the shifter, because the whole movement threw every gear is equally heavy?  thanks, btw.  

Problem solved.  An exhaust joint is leaking hot exhaust fumes right onto the shifting linkage under the car.   This is heating up that linkage and the metal is expanding and causing it to become sticky.