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The operating system is usually burned into the internal NOR flash. The files must contain a bootheader boot header to be automatically relocated into the internal predefined partitions. If you are using the Seco BSPs you do not have to care for generating those headers.
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Bootloader "manual" version
after entering the bootloader command prompt, type in those the commands:
:) ereg<CR>
:) boot mmc filename<CR>
:) fb<CR>
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