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