I've found that everywhere in autoconf scripts flags are used like:
$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&AS_MESSAGE_LOG_FD
while automake and libtool use flags in the other order:
$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS)
$(AM_CFLAGS) $(CFLAGS)
I agree that this should be made consistent, but before we change anything, we
need to check what the rules *built into GNU and BSD Make* do with CFLAGS and
CPPFLAGS (and also CXXFLAGS, OBJCFLAGS, etc) because those are much much harder
to get changed than anything in Automake or Autoconf, so we should aim to
harmonize everything with them.
Can you look into that please, Evgeny?