lilypond-book with multi-dir projects

[Graham Percival]

I wish we'd finished NR 1 ages ago, so that the AU would be in
better shape... oh well.

Has anybody used lilypond-book for large (100+ pages) documents?
In particular, I'm having trouble with .lytex files in
subdirectories.

thesis.tex
exercises/exercises.lytex
=> exercises/exercises.tex

The created exercises.tex contains filenames like
  \input lily-2df7c51698-systems.tex
which contain lines like
  \includegraphics{lily-2df7c51698-1}

These commands naturally fail when I try to use pdflatex on the
main thesis.tex, since those files aren't in the same directory.
Is there any way to get lilypond-book to automatically add
  mydir/
to all filenames?  Or does anybody have any better solutions?

I could hack up a post-lilypond-book python script to do
such things, but that feels like such a hack.  :(
I could also abandon lilypond-book and create/insert .eps files
directly, but that feels like even more of a hack.  :)

Cheers,
- Graham