I fixed my problem, with the help of some info here: http://arduino.cc/forum/index.php?action=printpage;topic=92364.0
I couldn't for the life of me find the avr include files that I needed to look at, because I think the entire avr directory tree was installed as "hidden". Once I uncovered it - by default, the include files are under /usr/lib/avr/include/avr - I found the file io.h, which includes iom2560.h for the Mega2560. iom2560.h then includes the very obscure file iomxx0_1.h. In THAT file, I added the line
#define __AVR_LIBC_DEPRECATED_ENABLE__ 1
near the bottom of the file, right before that flag is tested. If __AVR_LIBC_DEPRECATED_ENABLE__ is not defined, then a long list of #pragma's are run to "poison" certain references, including the ones that were flagged as "poisoned" during the compile, causing fatal errors. The Blink sketch uploads and operates just fine now on the Mega....I may have caused myself new problems down the road, but for now, I'm happy, and can move on to bigger and better things!
oscarB, I suspect that your error listing is caused by X11 on your Pi either having crashed, or not ever started. The IDE needs X11 to be running on the Pi, or the IDE won't start. I am actually logging on to the Pi from my Mac, using a remote shell over my local network - I use the Terminal in Mac OS, and run the ssh command with a -X flag. The -X flag starts X11 on the Pi....you can also use other means to start X11 on the Pi directly, such as the "startx" command. Hope this helps....