Hi Kadir,
as described on
https://wiki.paparazziuav.org/wiki/Flight_Plans#Waypoints you
can either set waypoint altitude AboveSeaLevel (hMSL) or
height which is relative to the ground_alt you set in your
flight plan (not a true AGL, as it is only relative to your
initial ground altitude and not to over the hill you might be
currently flying).
Internally waypoints are stored relative to your initial
reference point (either flight plan position/alt or updated
after NavSetGroundReferenceHere() was called).
Does that answer your question?
Cheers, Felix