It's actually even a little worse:
Any dependency on sources in another directory causes a simple "make
clean" in one directory to erase _all_ object files on that other one,
i.e. if docs/Makefile.am has
noinst_PROGRAMS = a
a_SOURCES = sub/a.c ../src/main.c
a_CPPFLAGS = -DFOO=BAR $(AM_CPPFLAGS)
then "make -C docs clean" does the following:
make: Entering directory '/cygdrive/c/prg/gp/am_bug/amhello-1.0/docs'
test -z "a.exe" || rm -f a.exe
rm -f *.o
rm -f ../src/*.o
rm -f sub/*.o
make: Leaving directory '/cygdrive/c/prg/gp/am_bug/amhello-1.0/docs'
But what logic would a "clean" in one sub project erase all the work
done in another?
With consequences like that, I think the (all but forced, now) option
"subdir-objects" needs to be reconsidered.