PACKAGE_EXTRA_ARCHS in the conf file gets overwritten by the tune-atom
include following it, preventing the atom BASE_PACKAGE_ARCH from being
included in the final PACKAGE_ARCHS and causing do_rootfs to fail.
Remove the atom BASE_PACKAGE_ARCH and PACKAGE_EXTRA_ARCHS in the conf
file and allow the values in tune-atom to be used as intended.

Fixes [BUGID #986].

Signed-off-by: Tom Zanussi <tom.zanussi@intel.com>