I agree that you'd have to be carrying a pretty light load to attempt full-on parkour moves. In the system we use in my campaigns parkour could be performed using a variety of skills/attribute checks - the skills of jumping, climbing and acrobatics would be the most obvious, along with Agility atribute checks; some martial art skills could be substituted for some or all of the above.
Our rules system is quite punishing so I find that players who know the system well will tend to avoid having their characters engage in activities like parkour unless they think they'll have a good chance of succeeding. Obviously jumping from rooftop to rooftop can have pretty disastrous consequences in the event of a catastrophic failure.
Skills related to parkour can also be used to attempt to mitigate the consequences of a fall or something similar, like bailing out of a moving vehicle for instance.
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