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You need to run ipodpatcher from the command line. See here for instructions: https://www.rockbox.org/wiki/IpodPatcherHowever, ipodpatcher can only dump the partitions visible on the storage, it can't access the raw NAND nor can it access the external ROM chip containing the bootloader.
What are you actually trying to achieve? For the Ipods the firmware files from Apple are linked in the wiki: https://www.rockbox.org/wiki/IpodManualRestore If you simply want a backup for possible restore after swapping disks you can use those files (I've restored my Ipod disk a couple of times that way -- mini2g that is)
If you're comfortable disassembling ARMv4, you can dump the ROM file in Rockbox and look at the initialization code to see what it expects from the NAND. This could be pretty difficult though. I'm not sure if anyone has studied the ROM very closely, that might be worth searching through google and our wiki to see. Another option would be to use a NAND programmer to copy the contents of the working NAND to the new NAND and see if that works. This might fail if the ROM is looking for specific models of NAND, or if it expects different chips to be configured in different ways.
I don't know what kernel options are.
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