Seems we just feed it to mkisofs as Fabianx once told me.
man mkisofs
-sort sort file
Sort file locations on the media. Sorting is controlled by a
file that contains pairs of filenames and sorting offset weight-
ing. If the weighting is higher, the file will be located
closer to the beginning of the media, if the weighting is lower,
the file will be located closer to the end of the media. There
must be only one space or tabs character between the filename
and the weight and the weight must be the last characters on a
line. The filename is taken to include all the characters up to,
but not including the last space or tab character on a line.
This is to allow for space characters to be in, or at the end of
a filename. This option does not sort the order of the file
names that appear in the ISO9660 directory. It sorts the order
in which the file data is written to the CD image - which may be
useful in order to optimize the data layout on a CD. See
README.sort for more details.
The other scripts tidy everything up quite nicely. Simple!