I've gotten farther, but I still don't have things working. I thought I'd post things at this point to see if anyone else has better success than I do or sees something that I'm missing. Here's what the state of things are so far:
-Able to TFTP kernel to SAM9G25-EK board.
-Able to load filesystem that I'm using on my SBC6045 eval board on the SAM9G25-EK using NFS.
I really haven't tested much else. To get to the same place I am (if that is your desire), do the following:
1. Get the following files, and place them all in the same directory:
a. Kernel version 3.0.4 from kernel.org (linux-3.0.4.tar.bz2).
b. The 3.0.0 kernel patch from this other forum post:
viewtopic.php/f,12/t,19631/ (3.0.0-at91.patch.bz2)
c. The 3.0.4 SAM9X5 patch attached to this post (3.0.4-at91-highly-exp.tar.bz2)
2. From a terminal in that directory, enter the following commands:
a. tar -jxvf linux-3.0.4.tar.bz2
b. cp -a 3.0.0-at91-patch.tar.bz2 linux-3.0.4
c. cp -a 3.0.4-at91-highly-exp.tar.bz2 linux-3.0.4
d. cd linux-3.0.4
e. tar -jxvf 3.0.0-at91-patch.tar.bz2
f. tar -jxvf 3.0.4-at91-highly-exp.tar.bz2
g. patch -p1 --ignore-whitespace < 3.0.0-at91.patch
h. for p in 3.0.4-at91-highly-exp/* ; do patch -p1 --ignore-whitespace < $p ; done
3. Build the patched kernel the way you normally would.
If you want to use the same configuration I've been using, grab the attached configuration (sam9g25-ek_myconfig.tar.bz2), extract the file and save it as .config. Otherwise, keep using the same configuration you've been using.
I have been attempting to get USART0 and USART3 up and going, but the kernel boot hangs when it tries to add these ports. It looks like it's trying to re-add the debug serial port and hangs there. If you aren't concerned with getting the serial ports working, then comment out lines 337 and 339 of linux-3.0.4/arch/arm/mach-at91/board-sam9x5-ek.c.
In modifying the 2.6.39 patch for SAM9x5 support, I removed patches that were already applied to the Linux 3.x kernel. I kept the file numbers the same to make it easier to see what I changed if you are making comparisons between the 2.6.39 patch and mine.
As the patch name describes, this patch is highly experimental. The patch installs with some fuzz and a lot has not been fully tested, but so far this seems the closest of anything that has been posted for adding SAM9x5 support to the Linux 3.x kernel. I'm willing to work with people to get this working and vetted.
-Bryan