Hi Michael,
  I've ran into a situation where I've needed to use your module. The problem I found with it is that it doesn't merge arrays, just replaces one with the other. I had a situation where I had two array references such as:-

$a1 = [undef, item2];
$a2 = [item1, undef];
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I was ending up with

$a3 = [item1, undef];
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When I wanted

$a3 = [item1, item2];
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I've written an update that merges the arrays if items are undef like the example above. So far I've only tested with LEFT_PRECEDENT, but I don't see why it wouldn't work well for the others.

My changes to LEFT_PRECEDENT:-

'LEFT_PRECEDENT' => {
       'SCALAR' => {
           'SCALAR' => sub { $_[0] },
           'ARRAY'  => sub { $_[0] },
           'HASH'   => sub { $_[0] },
       },
       'ARRAY' => {
           'SCALAR' => sub { [ @{$_[0]}, $_[1] ] },
           'ARRAY'  => sub { [ @{$_[0]}, @{$_[1]} ] },
           'HASH'   => sub { [ @{$_[0]}, values %{$_[1]} ] },
       },
       'HASH' => {
           'SCALAR' => sub { $_[0] },
           'ARRAY'  => sub { $_[0] },
           'HASH'   => sub { _merge_hashes( $_[0], $_[1] ) },
       },
   },
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New sub:-

sub _merge_arrays {
   my ( $left, $right ) = ( shift, shift );
   if( ref $left ne 'ARRAY' || ref $right ne 'ARRAY' ) {
       carp 'Arguments for _merge_arrays must be array references';
       return;
   }

   my $length = $#$left;
   $length = $#$right if ($#$right > $length);
     my @newarray;
   for (my $num = 0; $num <= $length; $num++) {
       if ( defined $left->[$num] && defined $right->[$num] ) {
           @newarray[ $num ]
               = merge ( $left->[ $num ], $right->[ $num] );
       }
       elsif ( defined $left->[$num] && !(defined $right->[$num]) ) {
           @newarray[ $num ]
               = $left->[ $num ];
       }
       elsif ( !(defined $left->[$num]) && defined $right->[$num] ) {
           @newarray[ $num ]
               = $right->[ $num ];
       }
       else {
           $newarray[$num] = $clone_behavior
               ? _my_clone( $left->[$num] ) : $left->[$num];
       }
   }#for     return \@newarray;
}
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I'm guessing that this would make a good option for people. I wont implement it fully as it's your module after all. But if you do it implement it I'd greatly appreciate a mention, love reading my name on CPAN ;)

By the way I noticed that there is now a Pure Perl Clone module that doesn't need to be required in so I guess that you could use one or the other depending on availability to fix your ActiveState Clone problem.

Hope this helps.