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I got linker script working in a different way. I think you need to include sections like *(.data) but also *(.text) as well as *(.text.*). I also added some section that I found floating around in the .map file. Their sizes are 0 so they didn't have any effect yet, but might in the future. (I also posted a comment on your blog about this). I didn't need to remove the AT >FLASH for this to work. My version is here: http://pastebin.com/AcxwFW6S