Oops, the patch that I committed worked right in the second run, but not
in the first run. Fixed:

2008-09-25  Bruno Haible  <[EMAIL PROTECTED]>

        * gnulib-tool (func_import): When computing the edits, consider not
        only the Makefile.ams that exist but also those that will be generated.

*** gnulib-tool.orig    2008-09-25 15:59:10.000000000 +0200
--- gnulib-tool 2008-09-25 15:57:51.000000000 +0200
***************
*** 2929,2940 ****
    fi
    func_note_Makefile_am_edit "" ACLOCAL_AMFLAGS "-I ${m4base}"
    {
!     # Find the first parent directory of $m4base that contains a Makefile.am.
      sed_last='s,^.*/\([^/][^/]*\)//*$,\1/,
  s,//*$,/,'
      sed_butlast='s,[^/][^/]*//*$,,'
      dir1="${m4base}/"; dir2=""
!     while test -n "$dir1" && test ! -f "${destdir}/${dir1}Makefile.am"; do
        dir2=`echo "$dir1" | sed -e "$sed_last"`"$dir2"
        dir1=`echo "$dir1" | sed -e "$sed_butlast"`
      done
--- 2929,2947 ----
    fi
    func_note_Makefile_am_edit "" ACLOCAL_AMFLAGS "-I ${m4base}"
    {
!     # Find the first parent directory of $m4base that contains or will contain
!     # a Makefile.am.
      sed_last='s,^.*/\([^/][^/]*\)//*$,\1/,
  s,//*$,/,'
      sed_butlast='s,[^/][^/]*//*$,,'
      dir1="${m4base}/"; dir2=""
!     while test -n "$dir1" \
!           && ! { test -f "${destdir}/${dir1}Makefile.am" \
!                  || test "${dir1}Makefile.am" = "$sourcebase/$makefile_am" \
!                  || test "./${dir1}Makefile.am" = "$sourcebase/$makefile_am" \
!                  || { test -n "$inctests" \
!                       && { test "${dir1}Makefile.am" = 
"$testsbase/$makefile_am" \
!                            || test "./${dir1}Makefile.am" = 
"$testsbase/$makefile_am"; }; }; }; do
        dir2=`echo "$dir1" | sed -e "$sed_last"`"$dir2"
        dir1=`echo "$dir1" | sed -e "$sed_butlast"`
      done



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