atl1: reorder atl1_main functions

Reorder functions in atl1_main into more logical groupings to make the
code easier to follow. This patch is large, but it's harmless; it neither
adds nor removes any functionality whatsoever.

Signed-off-by: Jay Cliburn <jacliburn@bellsouth.net>
Signed-off-by: Jeff Garzik <jeff@garzik.org>