Hi,
yes, I finally did it.
from the source code of the boot of altera and the one of "jakobjones", withing the folder of the makefile, just type in the command shell: "make clean all".
The makefile includes in the INCLUDES2 the folder where the system.h is, to take the BASE of the remote_system_upgrade.
From the files I took from "jakobjones", I changed the boot_loader.S and the boot_loader_epcs_bits_sii_siii_ciii.S. For example, when it reopens the epcs at byte_N, I do:
addi r_flash_ptr, r_reconfig_image_base, N
I read the remote system upgrade, and boot from the address 0x200000 if the reconfiguration register is not zero.
Finally, I create the .hex with:
elf2hex --width=32 --base=0x0 --end=0x3ff --input=obj/boot_loader_epcs.elf --output=epcs_flash_controller_0_boot_rom.hex --record=4 --lower
It works. Remember you have to do it again everytime you make a generate in the sopc, as it overwrites the file with the standard "epcs_flash_controller_0_boot_rom".
I've attached the makefile, boot_loader.h, boot_loader.S and boot_loader_epcs_bits_sii_siii_ciii.S. (sorry, I don´t have the winzip at this moment, I just added the .doc extension to upload the file, just throw it).
hope it helps,
Melo.