I've had the same problem with today's checkout. After I ran I think this is to be expected if you start with autogen.sh, since gnulib is so dynamic.
I keep gnulib and various other autotools files in CVS precisely so autogen.sh should not be necessary -- it should suffice to simply run configure. I'll update gnulib in due course. It would cause more trouble than it would solve to try to track it completely. Thanks, k
