how-to-make-a-clean-patch

Well, first make a file with a list of the files you've changed.

arch/arm/mach-at91rm9200/board-ecbat91.c
arch/arm/mach-at91rm9200/Kconfig
arch/arm/mach-at91rm9200/Makefile
arch/arm/tools/mach-types
drivers/net/arm/at91_ether.c
drivers/mmc/mmc.c
drivers/mmc/mmc_block.c
drivers/mmc/at91_mci.c

Then do this:

 cat file-list.txt | perl -nwe ' chomp; print "diff -urN linux-2.6.20.orig/$_ linux-2.6.20/$_\n" '

And it will show you the commands you need to create your patch. Just pipe to a sheel and redirect to your brand new patch.

 cat file-list.txt | perl -nwe ' chomp; print "diff -urN linux-2.6.20.orig/$_ linux-2.6.20/$_\n" ' | sh > 2.6.20.my.cool.patch