xdt-autogen: Set `aclocal` folders after running `libtoolize`

So that when AC_CONFIG_MACRO_DIRS is used in configure.ac.in and "${source_dir}/m4" is not created in autogen.sh before running xdt-autogen, aclocal is still launched with the right parameters.

Related to apps/mousepad!76 (closed), see in particular apps/mousepad!76 (comment 22749).