Makefile: Fix make index on FreeBSD 13

With recent main branch make index causes following warning message
on FreeeBSD 13.

make_index: Circular dependency loop found: glib-2.84.1_2,2 depends upon itself.

And it generates empty index file.

The issue seems to happen because /usr/libexec/make_index is used on
FreeBSD 13. So fix it by changing Makefile so Tools/make_index is
always used.

PR: 285999
Approved by: portmgr (implicit, just fix it)