Build problem w/ latest automake/autoconf

[John K. H. <hi...@al...>]

I'm having configure/automake trouble building the CVS head on Debian
even after upgrading my automake (to 1.8.3) and autoconf (to 2.59)
which upgrades usually fix these things...

The Makefile seems to concatenate together all the "configure.in" for
all the modules - even if I am not building them, into one big file
"configure.ac" which contains duplicate definitions from the various
modules:

     cat src/configure.in modules/wildcard/configure.in modules/regexp/configure.in modules/clx/new-clx/configure.in modules/postgresql/configure.in modules/dirkey/configure.in modules/syscalls/configure.in modules/oracle/configure.in modules/fastcgi/configure.in modules/berkeley-db/configure.in modules/pcre/configure.in ffcall/configure.in ffcall/avcall/configure.in ffcall/vacall/configure.in ffcall/trampoline/configure.in ffcall/callback/configure.in ffcall/callback/vacall_r/configure.in ffcall/callback/trampoline_r/configure.in utils/hln/configure.in libcharset/configure.in | grep -v AC_INIT | grep -v AC_OUTPUT >> configure.ac

Then this command fails:
	aclocal -I src/m4 --output=src/autoconf/aclocal.m4

w/ the error:

   configure.ac:344: error: `config.h' is already registered with AC_CONFIG_HEADERS.
   autoconf/status.m4:424: AC_CONFIG_HEADERS is expanded from...
   configure.ac:344: the top level
   autom4te: /usr/bin/m4 failed with exit status: 1
   aclocal: autom4te failed with exit status: 1
   make[1]: *** [src/autoconf/aclocal.m4] Error 1
   make[1]: Leaving directory `/u/hin/src/clisp'
   make: *** [../src/VERSION] Error 2

I looked at the "configure.ac" and it appears the line

	AC_CONFIG_HEADERS(config.h)

is drawn in from most of the various modules' configure.in ...  what
to do?  

... As quick fix I tried commenting out the redundant directives in
the configure.in files for just the modules I am building, but then
there are many, many other duplicates, such as

	AC_CONFIG_FILES([Makefile])

Is there a way to tell automake's "aclocal" to just ignore the
duplicates and keep going?

Or some way to fix the build environment?