A few comments, further cleanup. A few TODOs handled.

Penumbra/Mods/Manager/Mod.Manager.BasePath.cs

@@ -12,14 +12,19 @@ public partial class Mod
         public delegate void ModPathChangeDelegate( ModPathChangeType type, Mod mod, DirectoryInfo? oldDirectory,
             DirectoryInfo? newDirectory );
 
-        public event ModPathChangeDelegate? ModPathChanged;
+        public event ModPathChangeDelegate ModPathChanged;
 
+        // Rename/Move a mod directory.
+        // Updates all collection settings and sort order settings.
         public void MoveModDirectory( Index idx, DirectoryInfo newDirectory )
         {
             var mod = this[ idx ];
             // TODO
         }
 
+        // Delete a mod by its index.
+        // Deletes from filesystem as well as from internal data.
+        // Updates indices of later mods.
         public void DeleteMod( int idx )
         {
             var mod = this[ idx ];
@@ -41,9 +46,10 @@ public partial class Mod
                 --remainingMod.Index;
             }
 
-            ModPathChanged?.Invoke( ModPathChangeType.Deleted, mod, mod.BasePath, null );
+            ModPathChanged.Invoke( ModPathChangeType.Deleted, mod, mod.BasePath, null );
         }
 
+        // Load a new mod and add it to the manager if successful.
         public void AddMod( DirectoryInfo modFolder )
         {
             if( _mods.Any( m => m.BasePath.Name == modFolder.Name ) )
@@ -59,7 +65,22 @@ public partial class Mod
 
             mod.Index = _mods.Count;
             _mods.Add( mod );
-            ModPathChanged?.Invoke( ModPathChangeType.Added, mod, null, mod.BasePath );
+            ModPathChanged.Invoke( ModPathChangeType.Added, mod, null, mod.BasePath );
+        }
+
+        // Add new mods to NewMods and remove deleted mods from NewMods.
+        private void OnModPathChange( ModPathChangeType type, Mod mod, DirectoryInfo? oldDirectory,
+            DirectoryInfo? newDirectory )
+        {
+            switch( type )
+            {
+                case ModPathChangeType.Added:
+                    NewMods.Add( mod );
+                    break;
+                case ModPathChangeType.Deleted:
+                    NewMods.Remove( mod );
+                    break;
+            }
         }
     }
 }

Penumbra/Mods/Manager/Mod.Manager.Options.cs

@@ -197,6 +197,14 @@ public sealed partial class Mod
                 return;
             }
 
+            if( mod._groups[ groupIdx ].Count > 63 )
+            {
+                PluginLog.Error(
+                    $"Could not add option {option.Name} to {mod._groups[ groupIdx ].Name} for mod {mod.Name}, "
+                  + "since only up to 64 options are supported in one group." );
+                return;
+            }
+
             switch( mod._groups[ groupIdx ] )
             {
                 case SingleModGroup s:

Penumbra/Mods/Manager/Mod.Manager.Root.cs

@@ -11,16 +11,19 @@ public sealed partial class Mod
         public DirectoryInfo BasePath { get; private set; } = null!;
         public bool Valid { get; private set; }
 
-
         public event Action? ModDiscoveryStarted;
         public event Action? ModDiscoveryFinished;
 
+        // Change the mod base directory and discover available mods.
         public void DiscoverMods( string newDir )
         {
             SetBaseDirectory( newDir, false );
             DiscoverMods();
         }
 
+        // Set the mod base directory.
+        // If its not the first time, check if it is the same directory as before.
+        // Also checks if the directory is available and tries to create it if it is not.
         private void SetBaseDirectory( string newPath, bool firstTime )
         {
             if( !firstTime && string.Equals( newPath, Penumbra.Config.ModDirectory, StringComparison.InvariantCultureIgnoreCase ) )
@@ -59,8 +62,10 @@ public sealed partial class Mod
             }
         }
 
+        // Discover new mods.
         public void DiscoverMods()
         {
+            NewMods.Clear();
             ModDiscoveryStarted?.Invoke();
             _mods.Clear();
             BasePath.Refresh();

Penumbra/Mods/Manager/Mod.Manager.cs

@@ -6,16 +6,22 @@ namespace Penumbra.Mods;
 
 public sealed partial class Mod
 {
-    public sealed partial class Manager : IEnumerable< Mod >
+    public sealed partial class Manager : IReadOnlyList< Mod >
     {
+        // An easily accessible set of new mods.
+        // Mods are added when they are created or imported.
+        // Mods are removed when they are deleted or when they are toggled in any collection.
+        // Also gets cleared on mod rediscovery.
+        public readonly HashSet< Mod > NewMods = new();
+
         private readonly List< Mod > _mods = new();
 
+        public Mod this[ int idx ]
+            => _mods[ idx ];
+
         public Mod this[ Index idx ]
             => _mods[ idx ];
 
-        public IReadOnlyList< Mod > Mods
-            => _mods;
-
         public int Count
             => _mods.Count;
 
@@ -29,6 +35,7 @@ public sealed partial class Mod
         {
             SetBaseDirectory( modDirectory, true );
             ModOptionChanged += OnModOptionChange;
+            ModPathChanged   += OnModPathChange;
         }
     }
 }