The .version section should stay in the same place (last two bytes of flash memory in the chip), but the .text segment address will change for a longer bootloader. For a 1K bootloader on atmega328, you'd want to start at the 31k mark
BTW, I didn't have any problem adding EEPROM support (under BIG_BOOT for atmega1284, just by including <avr/eeprom.h> and using eeprom_write_byte() and eeprom_read_byte() (which are macros, so they shouldn't result in any special library requirements.)
the whole avr toolchain in the fedora repos seems to be somewhat different
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