Hi stevieb, you can move (rename) directories with File::Copy:

#!/usr/bin/perl
use strict;
use warnings;
use File::Copy 'mv';

mkdir( 'Project/src' ) or die $!;

mv('Project/lib', 'Project/src/lib' )  or die $!;
mv('Project/t',   'Project/src/apps' ) or die $!;

__END__
[download]

$ ls -lR Project
total 0
-rw-r--r--  1 nick  staff    0 Sep  4 09:20 Makefile.PL
drwxr-xr-x  3 nick  staff  102 Sep  4 09:21 lib
drwxr-xr-x  3 nick  staff  102 Sep  4 09:21 t

Project/lib:
total 0
-rw-r--r--  1 nick  staff  0 Sep  4 09:21 Modul.pm

Project/t:
total 0
-rw-r--r--  1 nick  staff  0 Sep  4 09:21 test
$
[download]

$ perl 1141027.pl
$
[download]

$ ls -lR Project
total 0
-rw-r--r--  1 nick  staff    0 Sep  4 09:20 Makefile.PL
drwxr-xr-x  4 nick  staff  136 Sep  4 09:26 src

Project/src:
total 0
drwxr-xr-x  3 nick  staff  102 Sep  4 09:21 apps
drwxr-xr-x  3 nick  staff  102 Sep  4 09:21 lib

Project/src/apps:
total 0
-rw-r--r--  1 nick  staff  0 Sep  4 09:21 test

Project/src/lib:
total 0
-rw-r--r--  1 nick  staff  0 Sep  4 09:21 Modul.pm
[download]