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    <p>So it turns out <code>Hash::Merge</code> was only mangling my data on Windows using an outdated version of the Clone module.</p> <p>With up-to-date versions (or on my Mac right off the bat) the following code does exactly what I need:</p> <pre><code>#!/usr/bin/env perl -w use strict; use JSON; use Hash::Merge qw( merge ); Hash::Merge::set_behavior('RIGHT_PRECEDENT'); # Load full config into hashref open (IN, "&lt;:utf8", "full-config.txt"); my $app_data; while(&lt;IN&gt;) {$app_data .= $_;} my $app_json = decode_json($app_data); close IN; # Sample portion of config options to override/extend my $app_override = '{"config": { "bookToolbar": { "bookmark": { "enabled":false }, "help": { "data": { "url":"aGreatHelpFile.html" }, "enabled":true }, "closeBook": { "enabled":true } } }, "pagelist":[ { "hasOnPageNotes" : true, "pageName" : "25", "hasTextMarkup" : true, "hasScreenReader" : false, "hasLinks" : false, "pageId" : "0025" } ] }'; my $app_override_hash = from_json($app_override, {utf8 =&gt; 1}); # Merge with right precedent, $app_json hash ref has everything we need. $app_json = merge( $app_json, $app_override_hash ); </code></pre> <p>I found this table exceptionally helpful to analyze the different precedence options in <code>Hash::Merge</code> (this is <a href="http://search.cpan.org/~dmuey/Hash-Merge-0.12/Merge.pm" rel="nofollow">straight from the docs</a>:</p> <pre><code> LEFT TYPE RIGHT TYPE LEFT_PRECEDENT RIGHT_PRECEDENT SCALAR SCALAR $a $b SCALAR ARRAY $a ( $a, @$b ) SCALAR HASH $a %$b ARRAY SCALAR ( @$a, $b ) $b ARRAY ARRAY ( @$a, @$b ) ( @$a, @$b ) ARRAY HASH ( @$a, values %$b ) %$b HASH SCALAR %$a $b HASH ARRAY %$a ( values %$a, @$b ) HASH HASH merge( %$a, %$b ) merge( %$a, %$b ) LEFT TYPE RIGHT TYPE STORAGE_PRECEDENT RETAINMENT_PRECEDENT SCALAR SCALAR $a ( $a ,$b ) SCALAR ARRAY ( $a, @$b ) ( $a, @$b ) SCALAR HASH %$b merge( hashify( $a ), %$b ) ARRAY SCALAR ( @$a, $b ) ( @$a, $b ) ARRAY ARRAY ( @$a, @$b ) ( @$a, @$b ) ARRAY HASH %$b merge( hashify( @$a ), %$b ) HASH SCALAR %$a merge( %$a, hashify( $b ) ) HASH ARRAY %$a merge( %$a, hashify( @$b ) ) HASH HASH merge( %$a, %$b ) merge( %$a, %$b ) </code></pre>
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