I notice that there are a lot of different aclocal directories under /usr/share:
$ ls -ld /usr/share/aclocal*
drwxr-xr-x 2 root root 4096 May 6 12:23 /usr/share/aclocal
drwxr-xr-x 2 root root 4096 May 6 12:29 /usr/share/aclocal-1.10
drwxr-xr-x 2 root root 4096 Dec 1 2006 /usr/share/aclocal-1.4
drwxr-xr-x 2 root root 4096 Dec 1 2006 /usr/share/aclocal-1.5
drwxr-xr-x 2 root root 4096 Dec 1 2006 /usr/share/aclocal-1.6
drwxr-xr-x 2 root root 4096 Dec 1 2006 /usr/share/aclocal-1.7
I wonder if this is somehow confusing autoreconf?
Libtool is only in aclocal:
$ find /usr/share/aclocal* -name libtool.m4
/usr/share/aclocal/libtool.m4