Remove files that are remade anyway.

Makefile.in prescribed using aclocal 1.16. The fix removes any
dependency on the autotool version.
Fixing bug 806.

autogen.sh

@@ -115,6 +115,10 @@ fi
     exit 1
 }
 
+echo "Removing files to be remade"
+rm -f Makefile.in aclocal.m4 ar-lib config.guess config.sub
+rm -f depcomp install-sh ltmain.sh missing ylwrap
+rm -r -f autom4te.cache
 
 echo "Running $LIBTOOLIZE"
 $LIBTOOLIZE --copy --force \