1) Is there anyone that can help us with the configuration needed on the airframe file so that the paparazzi communicates to the ground station through a serial port?
Does anyone has a working airframe file that uses direct communication through serial port?
Not quite sure what you mean by "direct communication through serial port". A serial cable instead of wireless xbees for testing on the ground?
2) I know that there is a way to connect the paparazzi directly to the computer without using the Xbees. How can you do that?
In that case you should make sure that you use the "transparent" and not the "xbee_api" protocol.
3) How can I change the COM ports that the Paparazzi uses to communicate? What are the options available?
On the ground segment side?
Just pass the appropriate device to the link agent with the "-d <device>" option.
e.g. default is usually
sw/ground_segment/tmtc/link -d /dev/ttyUSB0
Hope this helps.. I'm afraid I didn't fully understand where exactly your problems are..