Okay, here's what I've figured out about the listing provided as
supplement 4 of Thibault et al. on the _Nature Genetics_ website (it was
well-organized, but I wish there'd been a little more info at the top of
the thing -- it's nearly 3800 pages long!)
The lines are organized into four sections, by element type: XP, PB, RB,
Within each section, they're organized by chromosome arm: 4, then 2R,
3R, 2L, X, and 3L.
Finally, within each of these arm-subsections, they're in order by
position, with the insertion site given in genome position.
Hope this is useful to others.