Comment #15 on issue 1821 by percival.music.ca: GUB argument list too long
http://code.google.com/p/lilypond/issues/detail?id=1821
Judging from the logfile from comment 3:
http://lilypond.org/~graham/lilypond-test.log
it is indeed using absolute paths.
Note that the only people using GUB are Jan, me, sometimes Nils, and maybe
one or two people in openoffice.org or inkscape or something like that --
this isn't something aimed at casual users! That said, since this is
cropping up in the lys-to-tely.py file, I guess it's relevant for lilypond
itself rather than merely GUB.