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The bootloader is a small program to start up the main operating system. The Openmoko phones can use U-Boot or Qi as bootloaders. Qi is actively developed, while the Openmoko version of U-Boot is not.
The Neo FreeRunner has two bootloaders. The NOR Flash contains a version of U-Boot which cannot be modified. Therefore it is always available as a fallback, and the second bootloader can be modified without any risk. This bootloader can be booted into by pressing and holding the AUX button and then pressing the Power button.
Note that the NOR bootloader has a size limit of 2 MB for the kernel. The NAND u-boot loader has the same limit, but you could rather easily increase it by modifying the u-boot environment.