AVR Freaks

But .eeprom is based at 0x810000. Where are you making the adjustment to rebase that?

To give you an idea. When AS7 creates EEPROM  it does it with:

"C:\Program Files (x86)\Atmel\Studio\7.0\toolchain\avr8\avr8-gnu-toolchain\bin\avr-objcopy.exe" -j .eeprom  --set-section-flags=.eeprom=alloc,load --change-section-lma .eeprom=0  --no-change-warnings -O ihex "test.elf" "test.eep" || exit 0

note the -change-section-lma in that.

If I were a Linux user I would be using Mfile. The Mfile template has the equivalent:

%.eep: %.elf
	@echo
	@echo $(MSG_EEPROM) $@
	-$(OBJCOPY) -j .eeprom --set-section-flags=.eeprom="alloc,load" \
	--change-section-lma .eeprom=0 --no-change-warnings -O $(FORMAT) $< $@ || exit 0

I suggest you don't mess about with "roll your own" Makefile unless you know exactly how this toolchain works. All good IDEs will do the -change-section-lma thing and all decent Makefile templates will too.

The point is that AVR is Harvard and GCC is Von Neumann. So the multiple memory sections in an AVR have to be "flattened" to work in GCC. That happens in the linker script:

MEMORY
{
  text   (rx)   : ORIGIN = 0, LENGTH = __TEXT_REGION_LENGTH__
  data   (rw!x) : ORIGIN = 0x800060, LENGTH = __DATA_REGION_LENGTH__
  eeprom (rw!x) : ORIGIN = 0x810000, LENGTH = __EEPROM_REGION_LENGTH__
  fuse      (rw!x) : ORIGIN = 0x820000, LENGTH = __FUSE_REGION_LENGTH__
  lock      (rw!x) : ORIGIN = 0x830000, LENGTH = __LOCK_REGION_LENGTH__
  signature (rw!x) : ORIGIN = 0x840000, LENGTH = __SIGNATURE_REGION_LENGTH__
  user_signatures (rw!x) : ORIGIN = 0x850000, LENGTH = __USER_SIGNATURE_REGION_LENGTH__
}

The 0x810000 offset is applied to EEPROM here - it must be removed again later when you are doing things like extracting .eeprom from the ELF to make a .eep

But to preempt that:   http://alfred.sax.de/~joerg/mfile/

Mfile is actually an interactive Makefile editor. There is a GUI (in Tcl/Tkinter) that allows you to edit things but, to be honest, the most useful thing is simply makefile_template that comes with it. You can forget the other bits and just take a copy of that as "Makefile" and then hand edit it.

That template was put together by some of the original avr-gcc gurus and has a lot of their combined knowledge in it so it will "fix" a lot of the problems you might otherwise encounter if trying to make up this stuff as you go along.