Follow-up Comment #9, bug #28744 (project avrdude):

Sorry for the delay -- my mail filters got ahold of these notifications. 
Hopefully fixed.

I use a BIN file for programming.  I initially tried using HEX files but ran
into problems with offsets.  I put it on my todo list to track down those
problems but haven't had any time.  My makefile kicks out BINs for everything
too, so that made life easy.

The BOOT section is offset, and the hex files also have offsets.  I'm
guessing that the offsets aren't being taken into account.  A problem I have
with the programming algorithm is that there isn't a simple way to discern
memory areas when programming as "flash".  So if you do a "flash" program on a
hex file that offsets into the boot section there isn't an easy way to say "if
memaddr is in boot area use the boot write cmd".  The quick hack I did just
checks the section against "boot" and uses that.  I guess I could write up
some code that tries to find the "common" names of sections and builds up
address ranges for those.

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