Josh,

> I can see how what I wrote above might be misinterpreted.
> Here is exactly what I did:
>
> -generate src/ with VMMaker (do chmod a+x, etc.)
> -tried to build; got error described above
>
> -rm -fr src
> -generate src with VMMaker (do chmod a+x, etc.)
> -mv src origsrc
> -cp -r origsrc src
> -tried to build; did not get error described above
>
> I verified that the directories src/ and origsrc/ are the same with
> "diff -r".  When I try:
> -rm -fr src
> -mv origsrc src
> -try to build
>
> the error pops up again.  Wierd.

Not weird at all. First of all, does "../src/src/Makefile.in" exist? I bet
it doesn't. If not, then there's a simple way to get the error through using
cp:
	- cp -r origsrc src
	- 'touch' the make file causing the problem like in:
		find . -name Makefile -exec touch {}\;
	- try to build
I bet it's the modification stamp of some Makefile wrt to some other file
that (by chance) gets a different stamp with cp (mv is moving files and
keeping the dates but cp is creating new ones and thus modifying the date).

(NB: If I'm not totally wrong here, why would it be a misinterpretation to
point out that Make is just complaining about a non-existing file?! ;-)

Cheers,
  - Andreas