Solution:
In Debian/Ubuntu the serial ports are in group 'dialout.' However, user tomcat6 is not a member of group dialout, and consequently could not see the ports.
$ ls -l /dev/ttyS*
crw-rw---- 1 root dialout 4, 64 2011-03-23 20:42 /dev/ttyS0
crw-rw---- 1 root dialout 4, 65 2011-03-03 10:28 /dev/ttyS1
crw-rw---- 1 root dialout 4, 66 2011-03-03 10:28 /dev/ttyS2
crw-rw---- 1 root dialout 4, 67 2011-03-03 10:28 /dev/ttyS3
To fix the problem, user tomcat6 must be added to group dialout:
root@ubuntuserver# usermod -G dialout tomcat6
Now Tomcat6 can see the serial ports, but Mango will not report them until it is restarted.
To restart Mango:
root@ubuntuserver# /etc/init.d/tomcat6 restart
Stopping Tomcat servlet engine tomcat6 [ OK ]
Starting Tomcat servlet engine tomcat6
Now Mango shows the serial ports in the pulldown menu
When I searched for this in the forum, I had searched for 'NMEA.' Once I noticed the same 'missing ports' problem was also on the 'Modbus serial' data source page, I narrowed it to a serial port problem, and searched the forum for 'rxtx' and found out that [url=http://mango.serotoninsoftware.com/forum/posts/list/0/189.page#1362]'a reboot was mandatory,' so I restarted Tomcat.
[solved]
It would be useful to have a Mango wiki so that these issues can be organized and updated in a more structured manner than what a forum can support.