This screams "symlink" to me...

In your embperl files:

  use lib "/var/www/intranet/currently-in-use/lib"
[download]

And on the shell:

  $ ln -s /var/www/intranet/stable /var/www/intranet/currently-in-use
  
  .. time passes, switch to devel version ..
  
  $ rm /var/www/intranet/currently-in-use
  $ ln -s /var/www/intranet/devel /var/www/intranet/currently-in-use
[download]

blokhead