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The tools used are: ATMEL Flip 3.4.7 and AVR Studio 5.1

A) Failing to start application at boot:
A.1) I did program an application with AVR Studio 5.1,
     I compiled fine and I produced the "hex" file,
A.2) I did use ATMEL Flip 3.4.7 to write the "hex" file in flash:
     the program is not started by the bootloader;
     it seems the BOOTRST fuse is still zero.

B) Application at boot starts successfully:
B.1) If I use Flip 3.4.7 to write the "hex" file in flash
     of an alternative firmware to mine
     (firmware produced by a third party company)
B.2) and after I use always Flip to write my "hex" file in flash
     then everything is fine and my program is started.

Hence I worry about the way I produce the "hex" file with AVR Studio: do I need some specific option for the BOOTRST fuse to program it to start my application at reset ?

Federico Strati
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    Unlike certain other MCUs/toolchains the fuses are _not_ mapped into the address space of the HEX image written, which stores only the FLASH code image itself. You will either need to produce a compound image capable of storing multiple memory spaces, such as an ELF image, program the fuses manually from the IDE, or pass along separate HEX image or command-line option containing the fuse values. – doynax Apr 04 '16 at 16:32
  • yes, but is there a simple compiler linker option to say to the bootloader to start the application ? I do not understand why if compiled with default options the bootloader does not start my application... – Federico Strati Apr 05 '16 at 09:28

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