Otherwise too many things go wrong
(especially the creation of .deps btw: automake does garbage if you
include a local.mk which defines foo_SOURCES = $(prefix)/foo.cc: it
creates '$(prefix)/.deps', and I really mean single quotes: the very
string '$(prefix)' not interpolated (which it can't, of course)).
Yep. :-/
A while ago (I'm sure it's been more than a couple of years now),
ventured at changing depout.m4 to lift this limitation. I did have
something working back then, but it required invoking `make' at
config.status time. I dropped this idea as being unsuitable in the
presence of bugs (e.g., if `make' reinvokes configure, then there
can be an endless loop). Maybe I should go back and look again,
for example writing out a separate makefile could help...