Remove ExtraIds column and use OwnerId relationship for extras

- Remove ExtraIds property from BaseItemEntity and BaseItem
- Update RefreshExtras to query via OwnerId instead of cached ExtraIds
- Update GetExtras methods to query database via OwnerIds filter
- Add OwnerIds and ExtraTypes filter support to InternalItemsQuery
- Add filter handling in BaseItemRepository for new query options
- Update HasSpecialFeature/HasTrailer filters to use Extras relationship
- Add CleanupOrphanedExtras migration routine
- Add database migration to drop ExtraIds column

2 files changed, 121 insertions, 4 deletions

diff --git a/Jellyfin.Server/Migrations/Routines/CleanupOrphanedExtras.cs b/Jellyfin.Server/Migrations/Routines/CleanupOrphanedExtras.cs
new file mode 100644
index 0000000000..ffde30f0ca
--- /dev/null
+++ b/Jellyfin.Server/Migrations/Routines/CleanupOrphanedExtras.cs
@@ -0,0 +1,119 @@
+using System;
+using System.Linq;
+using System.Threading;
+using System.Threading.Tasks;
+using Jellyfin.Database.Implementations;
+using Jellyfin.Server.Migrations.Stages;
+using Jellyfin.Server.ServerSetupApp;
+using MediaBrowser.Controller.Channels;
+using MediaBrowser.Controller.Configuration;
+using MediaBrowser.Controller.Entities;
+using MediaBrowser.Controller.Library;
+using MediaBrowser.Controller.LiveTv;
+using MediaBrowser.Controller.MediaSegments;
+using MediaBrowser.Controller.Persistence;
+using Microsoft.EntityFrameworkCore;
+using Microsoft.Extensions.Logging;
+
+namespace Jellyfin.Server.Migrations.Routines;
+
+/// <summary>
+/// Removes orphaned extras (items with OwnerId pointing to non-existent items).
+/// Must run before EF migrations that add FK constraints on OwnerId.
+/// </summary>
+[JellyfinMigration("2026-01-13T23:00:00", nameof(CleanupOrphanedExtras), Stage = JellyfinMigrationStageTypes.CoreInitialisation)]
+[JellyfinMigrationBackup(JellyfinDb = true)]
+public class CleanupOrphanedExtras : IAsyncMigrationRoutine
+{
+    private readonly IStartupLogger<CleanupOrphanedExtras> _logger;
+    private readonly IDbContextFactory<JellyfinDbContext> _dbContextFactory;
+    private readonly ILibraryManager _libraryManager;
+
+    /// <summary>
+    /// Initializes a new instance of the <see cref="CleanupOrphanedExtras"/> class.
+    /// </summary>
+    /// <param name="logger">The startup logger.</param>
+    /// <param name="dbContextFactory">The database context factory.</param>
+    /// <param name="libraryManager">The library manager.</param>
+    /// <param name="itemRepository">The item repository.</param>
+    /// <param name="channelManager">The channel manager.</param>
+    /// <param name="recordingsManager">The recordings manager.</param>
+    /// <param name="mediaSourceManager">The media source manager.</param>
+    /// <param name="mediaSegmentManager">The media segments manager.</param>
+    /// <param name="configurationManager">The configuration manager.</param>
+    public CleanupOrphanedExtras(
+        IStartupLogger<CleanupOrphanedExtras> logger,
+        IDbContextFactory<JellyfinDbContext> dbContextFactory,
+        ILibraryManager libraryManager,
+        IItemRepository itemRepository,
+        IChannelManager channelManager,
+        IRecordingsManager recordingsManager,
+        IMediaSourceManager mediaSourceManager,
+        IMediaSegmentManager mediaSegmentManager,
+        IServerConfigurationManager configurationManager)
+    {
+        _logger = logger;
+        _dbContextFactory = dbContextFactory;
+        _libraryManager = libraryManager;
+        BaseItem.LibraryManager ??= libraryManager;
+        BaseItem.ItemRepository ??= itemRepository;
+        BaseItem.ChannelManager ??= channelManager;
+        BaseItem.MediaSourceManager ??= mediaSourceManager;
+        BaseItem.MediaSegmentManager ??= mediaSegmentManager;
+        BaseItem.ConfigurationManager ??= configurationManager;
+        Video.RecordingsManager ??= recordingsManager;
+    }
+
+    /// <inheritdoc/>
+    public async Task PerformAsync(CancellationToken cancellationToken)
+    {
+        var context = await _dbContextFactory.CreateDbContextAsync(cancellationToken).ConfigureAwait(false);
+        await using (context.ConfigureAwait(false))
+        {
+            var orphanedItemIds = await context.BaseItems
+                .Where(b => b.OwnerId.HasValue && !b.OwnerId.Value.Equals(Guid.Empty))
+                .Where(b => !context.BaseItems.Any(parent => parent.Id.Equals(b.OwnerId!.Value)))
+                .Select(b => b.Id)
+                .ToListAsync(cancellationToken)
+                .ConfigureAwait(false);
+
+            if (orphanedItemIds.Count == 0)
+            {
+                _logger.LogInformation("No orphaned extras found, skipping migration.");
+                return;
+            }
+
+            _logger.LogInformation("Found {Count} orphaned extras to remove", orphanedItemIds.Count);
+
+            var deleteOptions = new DeleteOptions
+            {
+                DeleteFileLocation = false // Extras don't have their own media files
+            };
+
+            var deletedCount = 0;
+            foreach (var itemId in orphanedItemIds)
+            {
+                cancellationToken.ThrowIfCancellationRequested();
+
+                var item = _libraryManager.GetItemById(itemId);
+                if (item is null)
+                {
+                    _logger.LogDebug("Item {ItemId} not found in library, may have been already deleted", itemId);
+                    continue;
+                }
+
+                try
+                {
+                    _libraryManager.DeleteItem(item, deleteOptions, notifyParentItem: false);
+                    deletedCount++;
+                }
+                catch (Exception ex)
+                {
+                    _logger.LogWarning(ex, "Failed to delete orphaned item {ItemId} ({ItemName})", item.Id, item.Name);
+                }
+            }
+
+            _logger.LogInformation("Successfully removed {Count} orphaned extras", deletedCount);
+        }
+    }
+}
diff --git a/Jellyfin.Server/Migrations/Routines/MigrateLibraryDb.cs b/Jellyfin.Server/Migrations/Routines/MigrateLibraryDb.cs
index 3150f70baa..2c96f00761 100644
--- a/Jellyfin.Server/Migrations/Routines/MigrateLibraryDb.cs
+++ b/Jellyfin.Server/Migrations/Routines/MigrateLibraryDb.cs
@@ -1176,10 +1176,8 @@ internal class MigrateLibraryDb : IDatabaseMigrationRoutine
             entity.ProductionLocations = productionLocations;
         }
 
-        if (reader.TryGetString(index++, out var extraIds))
-        {
-            entity.ExtraIds = extraIds;
-        }
+        // Skip ExtraIds column (removed - extras are now tracked via OwnerId relationship)
+        index++;
 
         if (reader.TryGetInt32(index++, out var totalBitrate))
         {