Index: source/tools/entity/Entity.pm
===================================================================
--- source/tools/entity/Entity.pm
+++ source/tools/entity/Entity.pm
@@ -11,15 +11,15 @@
 
 sub get_filename
 {
-    my ($vfspath) = @_;
-    my $fn = "$vfsroot/public/simulation/templates/$vfspath.xml";
+    my ($vfspath, $mod) = @_;
+    my $fn = "$vfsroot/$mod/simulation/templates/$vfspath.xml";
     return $fn;
 }
 
 sub get_file
 {
-    my ($vfspath) = @_;
-    my $fn = get_filename($vfspath);
+    my ($vfspath, $mod) = @_;
+    my $fn = get_filename($vfspath, $mod);
     open my $f, $fn or die "Error loading $fn: $!";
     local $/;
     return <$f>;
@@ -113,13 +113,35 @@
     }
 }
 
+sub get_main_mod
+{
+    my ($vfspath, $mods) = @_;
+    my @mods_list = split(/\|/, $mods);
+    my $main_mod = $mods_list[0];
+    my $fn = "$vfsroot/$main_mod/simulation/templates/$vfspath.xml";
+    if (not -e $fn)
+    {                    
+        for my $dep (@mods_list)
+        {       
+            $fn = "$vfsroot/$dep/simulation/templates/$vfspath.xml";
+            if (-e $fn)
+            {
+                $main_mod = $dep;
+                last;
+            }
+        }
+    }
+    return $main_mod;
+}
+
 sub load_inherited
 {
-    my ($vfspath) = @_;
-    my $layer = load_xml($vfspath, get_file($vfspath));
+    my ($vfspath, $mods) = @_;
+    my $main_mod = get_main_mod($vfspath, $mods);
+    my $layer = load_xml($vfspath, get_file($vfspath, $main_mod));
 
     if ($layer->{Entity}{'@parent'}) {
-        my $parent = load_inherited($layer->{Entity}{'@parent'}{' content'});
+        my $parent = load_inherited($layer->{Entity}{'@parent'}{' content'}, $mods);
         apply_layer($parent->{Entity}, $layer->{Entity});
         return $parent;
     } else {
@@ -129,17 +151,18 @@
 
 sub find_entities
 {
+    my ($modName) = @_;
     my @files;
     my $find_process = sub {
         return $File::Find::prune = 1 if $_ eq '.svn';
         my $n = $File::Find::name;
         return if /~$/;
         return unless -f $_;
-        $n =~ s~\Q$vfsroot\E/public/simulation/templates/~~;
+        $n =~ s~\Q$vfsroot\E/$modName/simulation/templates/~~;
         $n =~ s/\.xml$//;
         push @files, $n;
     };
-    find({ wanted => $find_process }, "$vfsroot/public/simulation/templates");
+    find({ wanted => $find_process }, "$vfsroot/$modName/simulation/templates");
 
     return @files;
 }
Index: source/tools/entity/checkrefs.pl
===================================================================
--- source/tools/entity/checkrefs.pl
+++ source/tools/entity/checkrefs.pl
@@ -4,39 +4,84 @@
 use File::Find;
 use XML::Simple;
 use JSON;
+use Getopt::Long qw(GetOptions);
 
+use lib ".";
 use Entity;
+ 
+GetOptions ( 
+    '--check-map-xml' => \(my $checkMapXml = 0),
+    '--check-unused' => \(my $checkUnused = 0),
+    '--validate-templates' => \(my $validateTemplates = 0),
+    '--root-actors' => \(my $rootActors = 0),
+    '--mod-to-check=s' => \(my $modToCheck = "public")
+);
 
-use constant CHECK_MAPS_XML => 0;
-use constant ROOT_ACTORS => 1;
-
 my @files;
 my @roots;
 my @deps;
 
+
 my $vfsroot = '../../../binaries/data/mods';
+my $mods = get_mod_dependencies_string($modToCheck);
+my $mod_list_string = $modToCheck;
+if ($mods ne "")
+{
+   $mod_list_string =  $mod_list_string."|$mods";
+}
+$mod_list_string =  $mod_list_string."|mod";
+print("Checking $modToCheck\'s integrity. \n");
+print("The following mod(s) will be loaded: $mod_list_string. \n");
+my @mods_list = split(/\|/, "$mod_list_string");
 
-sub vfs_to_physical
+sub get_mod_dependencies
 {
-    my ($vfspath) = @_;
-    my $fn = "$vfsroot/public/$vfspath";
-    if (not -e $fn)
-    {
-        $fn = "$vfsroot/mod/$vfspath";
+    my ($mod) = @_;
+    my $modjson = parse_json_file_full_path("$vfsroot/$mod/mod.json");
+    my $modjsondeps = $modjson->{'dependencies'};
+    for my $dep (@{$modjsondeps})
+    {       
+        # 0ad's folder isn't named like the mod.
+        if(index($dep, "0ad") != -1)
+        {
+            $dep = "public";
+        }
     }
-    return $fn;
+
+    return $modjsondeps;   
 }
 
+sub get_mod_dependencies_string
+{
+    my ($mod) = @_;
+    return join( '|',@{get_mod_dependencies($mod)});
+}
+
+sub vfs_to_physical
+{
+    my ($vfsPath) = @_;
+    my $fn = vfs_to_relative_to_mods($vfsPath);
+    return "$vfsroot/$fn";
+}
+
 sub vfs_to_relative_to_mods
 {
-    my ($vfspath) = @_;
-    my $fn = "public/$vfspath";
-    return $fn;
+    my ($vfsPath) = @_;
+
+    for my $dep (@mods_list)
+    {
+        my $fn = "$dep/$vfsPath";
+
+        if (-e "$vfsroot/$fn")
+        {
+            return $fn;
+        }
+    }
 }
 
 sub find_files
 {
-    my ($vfspath, $extn) = @_;
+    my ($vfsPath, $extn) = @_;
     my @files;
     my $find_process = sub {
         return $File::Find::prune = 1 if $_ eq '.svn';
@@ -44,24 +89,33 @@
         return if /~$/;
         return unless -f $_;
         return unless /\.($extn)$/;
-        $n =~ s~\Q$vfsroot\E/(public|mod)/~~;
+        $n =~ s~\Q$vfsroot\E/($mod_list_string)/~~;
         push @files, $n;
     };
-    find({ wanted => $find_process }, "$vfsroot/public/$vfspath");
-    find({ wanted => $find_process }, "$vfsroot/mod/$vfspath") if -d "$vfsroot/mod/$vfspath";
 
+    for my $dep (@mods_list)
+    {              
+        find({ wanted => $find_process },"$vfsroot/$dep/$vfsPath") if -d "$vfsroot/$dep/$vfsPath";    
+    }
+    
     return @files;
 }
 
-sub parse_json_file
+sub parse_json_file_full_path
 {
     my ($vfspath) = @_;
-    open my $fh, vfs_to_physical($vfspath) or die "Failed to open '$vfspath': $!";
+    open my $fh, $vfspath or die "Failed to open '$vfspath': $!";
     # decode_json expects a UTF-8 string and doesn't handle BOMs, so we strip those
     # (see http://trac.wildfiregames.com/ticket/1556)
     return decode_json(do { local $/; my $file = <$fh>; $file =~ s/^\xEF\xBB\xBF//; $file });
 }
 
+sub parse_json_file
+{
+    my ($vfspath) = @_;
+    return parse_json_file_full_path(vfs_to_physical($vfspath))
+}
+
 sub add_entities
 {
     print "Loading entities...\n";
@@ -73,8 +127,7 @@
     {
         my $path = "simulation/templates/$f.xml";
         push @files, $path;
-        my $ent = Entity::load_inherited($f);
-
+        my $ent = Entity::load_inherited($f, "$mod_list_string");
         push @deps, [ $path, "simulation/templates/" . $ent->{Entity}{'@parent'}{' content'} . ".xml" ] if $ent->{Entity}{'@parent'};
 
         if ($f !~ /^template_/)
@@ -103,12 +156,32 @@
 
             if ($ent->{Entity}{Identity})
             {
-                push @deps, [ $path, "art/textures/ui/session/portraits/" . $ent->{Entity}{Identity}{Icon}{' content'} ] if $ent->{Entity}{Identity}{Icon};
+                push @deps, [ $path, "art/textures/ui/session/portraits/" . $ent->{Entity}{Identity}{Icon}{' content'} ] if $ent->{Entity}{Identity}{Icon} and $ent->{Entity}{Identity}{Icon}{' content'} ne '';
             }
         }
     }
 }
 
+sub push_variant_dependencies
+{  
+    my ($variant, $f) = @_;
+    push @deps, [ $f, "art/variants/$variant->{file}" ] if $variant->{file};
+    push @deps, [ $f, "art/meshes/$variant->{mesh}" ] if $variant->{mesh};
+    push @deps, [ $f, "art/particles/$variant->{particles}{file}" ] if $variant->{particles}{file};
+    for my $tex (@{$variant->{textures}{texture}})
+    {
+        push @deps, [ $f, "art/textures/skins/$tex->{file}" ] if $tex->{file};
+    }
+    for my $prop (@{$variant->{props}{prop}})
+    {
+        push @deps, [ $f, "art/actors/$prop->{actor}" ] if $prop->{actor};
+    }
+    for my $anim (@{$variant->{animations}{animation}})
+    {
+        push @deps, [ $f, "art/animation/$anim->{file}" ] if $anim->{file};
+    }
+}
+
 sub add_actors
 {
     print "Loading actors...\n";
@@ -118,7 +191,7 @@
     {
         push @files, $f;
 
-        push @roots, $f if ROOT_ACTORS;
+        push @roots, $f if $rootActors;
 
         my $actor = XMLin(vfs_to_physical($f), ForceArray => [qw(group variant texture prop animation)], KeyAttr => []) or die "Failed to parse '$f': $!";
 
@@ -126,20 +199,7 @@
         {
             for my $variant (@{$group->{variant}})
             {
-                push @deps, [ $f, "art/meshes/$variant->{mesh}" ] if $variant->{mesh};
-                push @deps, [ $f, "art/particles/$variant->{particles}{file}" ] if $variant->{particles}{file};
-                for my $tex (@{$variant->{textures}{texture}})
-                {
-                    push @deps, [ $f, "art/textures/skins/$tex->{file}" ] if $tex->{file};
-                }
-                for my $prop (@{$variant->{props}{prop}})
-                {
-                    push @deps, [ $f, "art/actors/$prop->{actor}" ] if $prop->{actor};
-                }
-                for my $anim (@{$variant->{animations}{animation}})
-                {
-                    push @deps, [ $f, "art/animation/$anim->{file}" ] if $anim->{file};
-                }
+                push_variant_dependencies($variant, $f);
             }
         }
 
@@ -147,6 +207,21 @@
     }
 }
 
+
+sub add_variants
+{
+    print "Loading variants...\n";
+    my @variantfiles = find_files('art/variants', 'xml');
+
+    for my $f (sort @variantfiles)
+    {
+        push @files, $f;
+        push @roots, $f if $rootActors;
+        my $variant = XMLin(vfs_to_physical($f), ForceArray => [qw(texture prop animation)], KeyAttr => []) or die "Failed to parse '$f': $!";       
+        push_variant_dependencies($variant, $f);
+    }
+}
+
 sub add_art
 {
     print "Loading art files...\n";
@@ -193,10 +268,7 @@
     push @mapfiles, find_files('maps/skirmishes', 'xml');
     for my $f (sort @mapfiles)
     {
-        print "  $f\n";
-
         push @files, $f;
-
         push @roots, $f;
 
         my $map = XMLin(vfs_to_physical($f), ForceArray => [qw(Entity)], KeyAttr => []) or die "Failed to parse '$f': $!";
@@ -435,14 +507,21 @@
 
     for my $f (sort @rmsdefs)
     {
+        if ($f =~ /^maps\/random\/rmbiome/)
+        {
+            next;
+        }
+
         push @files, $f;
 
         push @roots, $f;
 
         my $rms = parse_json_file($f);
+        if($rms->{settings}{Script})
+        {
+            push @deps, [ $f, "maps/random/" . $rms->{settings}{Script} ];
+        }
 
-        push @deps, [ $f, "maps/random/" . $rms->{settings}{Script} ];
-
         # Map previews
         push @deps, [ $f, "art/textures/ui/session/icons/mappreview/" . $rms->{settings}{Preview} ] if $rms->{settings}{Preview};
     }
@@ -506,6 +585,7 @@
     for my $f (sort keys %revdeps)
     {
         next if exists $files{$f};
+
         warn "Missing file '$f' referenced by: " . (join ', ', map "'$_'", map vfs_to_relative_to_mods($_), sort @{$revdeps{$f}}) . "\n";
 
         if (exists $lcfiles{lc $f})
@@ -517,6 +597,7 @@
 
 sub check_unused
 {
+    my ($modName) = @_; 
     my %reachable;
     @reachable{@roots} = ();
 
@@ -536,46 +617,42 @@
         last if @newreachable == 0;
         @reachable{@newreachable} = ();
     }
+    my $terrains = "$modName/art/terrains/";
+    my $random = "$modName/maps/random/";
+    my $materials = "$modName/art/materials/";
 
     for my $f (sort @files)
     {
-        next if exists $reachable{$f};
-        warn "Unused file '" . vfs_to_relative_to_mods($f) . "'\n";
+        my $fullPath = vfs_to_relative_to_mods($f);
+        next if exists $reachable{$f} || (
+         index($fullPath, $terrains) != -1 ||
+         index($fullPath, $random) != -1 ||
+         index($fullPath, $materials) != -1);
+            warn "Unused file '" . $fullPath . "'\n";
     }
 }
 
 
-add_maps_xml() if CHECK_MAPS_XML;
-
+add_maps_xml() if $checkMapXml;
 add_maps_pmp();
-
 add_entities();
-
 add_actors();
-
+add_variants();
 add_art();
-
 add_materials();
-
 add_particles();
-
 add_soundgroups();
 add_audio();
-
 add_gui_xml();
 add_gui_data();
-
 add_civs();
-
 add_rms();
-
 add_techs();
-
 add_terrains();
 
-# TODO: add non-skin textures, and all the references to them
-
 print "\n";
 check_deps();
 print "\n";
-check_unused();
+check_unused($modToCheck) if $checkUnused;
+print "\n";
+system("perl ../xmlvalidator/validate.pl") if $validateTemplates;
Index: source/tools/entity/creationgraph.pl
===================================================================
--- source/tools/entity/creationgraph.pl
+++ source/tools/entity/creationgraph.pl
@@ -1,9 +1,10 @@
 use strict;
 use warnings;
 
+use lib ".";
 use Entity;
 
-my @files = Entity::find_entities();
+my @files = Entity::find_entities("public");
 
 my %files = map +($_ => 1), @files;
 
@@ -13,7 +14,7 @@
 for my $f (sort @files) {
     next if $f =~ /^template_/;
     print "# $f...\n";
-    my $ent = Entity::load_inherited($f);
+    my $ent = Entity::load_inherited($f, "public");
 
     if ($ent->{Entity}{Builder}) {
         my $ents = $ent->{Entity}{Builder}{Entities}{' content'};
Index: source/tools/entity/entvalidate.pl
===================================================================
--- source/tools/entity/entvalidate.pl
+++ source/tools/entity/entvalidate.pl
@@ -3,6 +3,7 @@
 
 use XML::LibXML;
 
+use lib ".";
 use Entity;
 
 my $rngschema = XML::LibXML::RelaxNG->new(location => '../../../binaries/system/entity.rng');
@@ -49,7 +50,7 @@
 
 sub check_all
 {
-    my @files = Entity::find_entities();
+    my @files = Entity::find_entities("public");
 
     my $count = 0;
     my $failed = 0;