Made a quick and dirty conversion of the windows script to a linux one. Tested on arch linux but should work on every distro.
@Echo OFF
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000002/00000049
wait
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000202/0000000B
wait
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000102/00000016
wait
cat 00000049 0000000B 00000016 > firmware.bin
rm 00000049
rm 0000000B
rm 00000016
wait
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000002/00000049
wait
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000202/0000000B
wait
wget http://nus.cdn.c.shop.nintendowifi.net/ccs/download/0004013800000102/00000016
wait
cat 00000049 0000000B 00000016 > firmware.bin
rm 00000049
rm 0000000B
rm 00000016
wait