DynamoDS
diff --git a/‎src/DynamoCoreWpf/ViewModels/PackageManager/PublishPackageViewModel.cs
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+22-26Lines changed: 22 additions & 26 deletions b/‎src/DynamoCoreWpf/ViewModels/PackageManager/PublishPackageViewModel.cs
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+22-26Lines changed: 22 additions & 26 deletions
@@ -895,8 +895,9 @@ public bool RetainFolderStructureOverride
         /// <summary>
         /// The root directory of the package
         /// </summary>
-        private string CurrentPackageDirectory { get; set; }
+        private IEnumerable<string> CurrentPackageRootDirectories { get; set; }
         private static MetadataLoadContext sharedMetaDataLoadContext = null;
+
         /// <summary>
         /// A shared MetaDataLoadContext that is used for assembly inspection during package publishing.
         /// This member is shared so the behavior is similar to the ReflectionOnlyLoadContext this is replacing.
@@ -1073,34 +1074,30 @@ internal List<PackageItemRootViewModel> BindParentToChild(Dictionary<string, Pac
             }
 
             // Only add the folder items, they contain the files
-            var updatedItems = GetRootItems(items);
+            var updatedItems = OrganizePackageRootItems(items);
             return updatedItems;
         }
 
         /// <summary>
-        /// Gets the list PackageItemRootViewModel items which will be at the root directory of the package with all the child items.
+        /// Organizes package items into root items based on common paths and hierarchical structure.
+        /// This includes determining root items, establishing parent-child relationships, and collecting all child items.
         /// </summary>
-        /// <param name="items"></param>
-        /// <returns></returns>
-        private List<PackageItemRootViewModel> GetRootItems(Dictionary<string, PackageItemRootViewModel> items)
+        /// <param name="items">A dictionary of package item keys and their corresponding PackageItemRootViewModel objects.</param>
+        /// <returns>A list of PackageItemRootViewModel items representing the organized root items and their child items.</returns>
+        private List<PackageItemRootViewModel> OrganizePackageRootItems(Dictionary<string, PackageItemRootViewModel> items)
         {
             var rootItems = items.Values.Where(x => !x.isChild).ToList();
             if (!rootItems.Any()) return rootItems;
 
             var roots = new List<PackageItemRootViewModel>();
+                      
+            var commonPaths = GetCommonPaths(items.Keys.ToArray());
+            if (commonPaths == null) return null;
 
-            if (CurrentPackageDirectory != null)
-            {
-                roots.Add(new PackageItemRootViewModel(CurrentPackageDirectory));
-            }
-            else
-            {
-                var commonPaths = GetCommonPaths(items.Keys.ToArray());
-                if (commonPaths == null) return null;
+            CurrentPackageRootDirectories = commonPaths;
 
-                // Add a new root item for each common path found
-                commonPaths.ForEach(p => roots.Add(new PackageItemRootViewModel(p)));
-            }
+            // Add a new root item for each common path found
+            commonPaths.ForEach(p => roots.Add(new PackageItemRootViewModel(p)));
 
             // Check each root item and create any missing connections
             foreach (var item in rootItems)
@@ -1532,7 +1529,7 @@ internal static PublishPackageViewModel FromLocalPackage(DynamoViewModel dynamoV
                 CopyrightHolder = pkg.CopyrightHolder,
                 CopyrightYear = pkg.CopyrightYear,
                 IsPublishFromLocalPackage = true,
-                CurrentPackageDirectory = pkg.RootDirectory,
+                CurrentPackageRootDirectories = new List<string> { pkg.RootDirectory },
                 //default retain folder structure to true when publishing a new version from local.
                 RetainFolderStructureOverride = retainFolderStructure
             };
@@ -2270,7 +2267,7 @@ private void Submit()
             {
                 // begin submission
                 var pmExtension = dynamoViewModel.Model.GetPackageManagerExtension();
-                var handle = pmExtension.PackageManagerClient.PublishAsync(Package, RetainFolderStructureOverride ? updatedFiles : contentFiles, MarkdownFiles, IsNewVersion, RetainFolderStructureOverride);
+                var handle = pmExtension.PackageManagerClient.PublishAsync(Package, RetainFolderStructureOverride ? updatedFiles : contentFiles, MarkdownFiles, IsNewVersion, CurrentPackageRootDirectories, RetainFolderStructureOverride);
 
                 // start upload
                 Uploading = true;
@@ -2365,11 +2362,7 @@ private void PublishLocally()
                     var remapper = new CustomNodePathRemapper(DynamoViewModel.Model.CustomNodeManager,
                         DynamoModel.IsTestMode);
                     var builder = new PackageDirectoryBuilder(new MutatingFileSystem(), remapper);
-                    if (string.IsNullOrEmpty(Package.RootDirectory))
-                    {
-                        Package.RootDirectory = CurrentPackageDirectory;
-                    }
-                    builder.BuildRetainDirectory(Package, publishPath, updatedFiles, MarkdownFiles);
+                    builder.BuildRetainDirectory(Package, publishPath, CurrentPackageRootDirectories, updatedFiles, MarkdownFiles);
                     UploadState = PackageUploadHandle.State.Uploaded;
                 }
                 else
@@ -2770,11 +2763,11 @@ internal PackageItemRootViewModel GetExistingRootItemViewModel(string publishPat
         {
             if (!PackageContents.Any()) return null;
             if (PackageContents.Count(x => x.DependencyType.Equals(DependencyType.Folder)) == 1) {
-                // If there is only one root item, nest it under the new root package folder
+                // If there is only one root item, this root item becomes the new folder
                 var item = PackageContents.First(x => x.DependencyType.Equals(DependencyType.Folder));
 
                 item = new PackageItemRootViewModel(Path.Combine(publishPath, packageName));
-                item.AddChildren(new List<PackageItemRootViewModel> { PackageContents.First() } );
+                item.AddChildren( PackageContents.First().ChildItems.ToList() );
 
                 return item;
             }
@@ -2783,6 +2776,9 @@ internal PackageItemRootViewModel GetExistingRootItemViewModel(string publishPat
             var rootItem = new PackageItemRootViewModel(Path.Combine(publishPath, packageName));
             foreach(var item in PackageContents)
             {
+                // Skip 'bare' custom nodes, they will be represented by their CustomNodePreview counterparts
+                if(item.DependencyType.Equals(DependencyType.CustomNode)) { continue; }
+
                 item.isChild = true;
                 rootItem.AddChildren(item);
             }