Now that was a lot of work.

Penumbra/Api/Api/ModSettingsApi.cs

@@ -11,6 +11,7 @@
 using Penumbra.Mods.Groups;
 using Penumbra.Mods.Manager;
 using Penumbra.Mods.Settings;
+using Penumbra.Mods.SubMods;
 using Penumbra.Services;
 
 namespace Penumbra.Api.Api;
@@ -254,7 +255,7 @@ private void OnModPathChange(ModPathChangeType type, Mod mod, DirectoryInfo? _1,
     private void OnModSettingChange(ModCollection collection, ModSettingChange type, Mod? mod, Setting _1, int _2, bool inherited)
         => ModSettingChanged?.Invoke(type, collection.Id, mod?.ModPath.Name ?? string.Empty, inherited);
 
-    private void OnModOptionEdited(ModOptionChangeType type, Mod mod, int groupIndex, int optionIndex, int moveIndex)
+    private void OnModOptionEdited(ModOptionChangeType type, Mod mod, IModGroup? group, IModOption? option, IModDataContainer? container, int moveIndex)
     {
         switch (type)
         {

Penumbra/Collections/Cache/CollectionCacheManager.cs

@@ -7,8 +7,10 @@
 using Penumbra.Interop.ResourceLoading;
 using Penumbra.Meta;
 using Penumbra.Mods;
+using Penumbra.Mods.Groups;
 using Penumbra.Mods.Manager;
 using Penumbra.Mods.Settings;
+using Penumbra.Mods.SubMods;
 using Penumbra.Services;
 using Penumbra.String.Classes;
 
@@ -257,7 +259,7 @@ private void RemoveCache(ModCollection? collection)
     }
 
     /// <summary> Prepare Changes by removing mods from caches with collections or add or reload mods. </summary>
-    private void OnModOptionChange(ModOptionChangeType type, Mod mod, int groupIdx, int optionIdx, int movedToIdx)
+    private void OnModOptionChange(ModOptionChangeType type, Mod mod, IModGroup? group, IModOption? option, IModDataContainer? container, int movedToIdx)
     {
         if (type is ModOptionChangeType.PrepareChange)
         {

Penumbra/Collections/Manager/CollectionStorage.cs

@@ -4,8 +4,10 @@
 using Penumbra.Communication;
 using Penumbra.Mods;
 using Penumbra.Mods.Editor;
+using Penumbra.Mods.Groups;
 using Penumbra.Mods.Manager;
 using Penumbra.Mods.Settings;
+using Penumbra.Mods.SubMods;
 using Penumbra.Services;
 
 namespace Penumbra.Collections.Manager;
@@ -290,15 +292,15 @@ private void OnModPathChange(ModPathChangeType type, Mod mod, DirectoryInfo? old
     }
 
     /// <summary> Save all collections where the mod has settings and the change requires saving. </summary>
-    private void OnModOptionChange(ModOptionChangeType type, Mod mod, int groupIdx, int optionIdx, int movedToIdx)
+    private void OnModOptionChange(ModOptionChangeType type, Mod mod, IModGroup? group, IModOption? option, IModDataContainer? container, int movedToIdx)
     {
         type.HandlingInfo(out var requiresSaving, out _, out _);
         if (!requiresSaving)
             return;
 
         foreach (var collection in this)
         {
-            if (collection.Settings[mod.Index]?.HandleChanges(type, mod, groupIdx, optionIdx, movedToIdx) ?? false)
+            if (collection.Settings[mod.Index]?.HandleChanges(type, mod, group, option, movedToIdx) ?? false)
                 _saveService.QueueSave(new ModCollectionSave(_modStorage, collection));
         }
     }

Penumbra/Communication/ModOptionChanged.cs

@@ -1,8 +1,10 @@
 using OtterGui.Classes;
-using Penumbra.Api;
 using Penumbra.Api.Api;
 using Penumbra.Mods;
+using Penumbra.Mods.Groups;
 using Penumbra.Mods.Manager;
+using Penumbra.Mods.SubMods;
+using static Penumbra.Communication.ModOptionChanged;
 
 namespace Penumbra.Communication;
 
@@ -11,22 +13,23 @@ namespace Penumbra.Communication;
 /// <list type="number">
 ///     <item>Parameter is the type option change. </item>
 ///     <item>Parameter is the changed mod. </item>
-///     <item>Parameter is the index of the changed group inside the mod. </item>
-///     <item>Parameter is the index of the changed option inside the group or -1 if it does not concern a specific option. </item>
-///     <item>Parameter is the index of the group an option was moved to. </item>
+///     <item>Parameter is the changed group inside the mod. </item>
+///     <item>Parameter is the changed option inside the group or null if it does not concern a specific option. </item>
+///     <item>Parameter is the changed data container inside the group or null if it does not concern a specific data container. </item>
+///     <item>Parameter is the index of the group or option moved or deleted from. </item>
 /// </list> </summary>
 public sealed class ModOptionChanged()
-    : EventWrapper<ModOptionChangeType, Mod, int, int, int, ModOptionChanged.Priority>(nameof(ModOptionChanged))
+    : EventWrapper<ModOptionChangeType, Mod, IModGroup?, IModOption?, IModDataContainer?, int, Priority>(nameof(ModOptionChanged))
 {
     public enum Priority
     {
-        /// <seealso cref="PenumbraApi.OnModOptionEdited"/>
+        /// <seealso cref="ModSettingsApi.OnModOptionEdited"/>
         Api = int.MinValue,
 
         /// <seealso cref="Collections.Cache.CollectionCacheManager.OnModOptionChange"/>
         CollectionCacheManager = -100,
 
-        /// <seealso cref="Mods.Manager.ModCacheManager.OnModOptionChange"/>
+        /// <seealso cref="ModCacheManager.OnModOptionChange"/>
         ModCacheManager = 0,
 
         /// <seealso cref="UI.AdvancedWindow.ItemSwapTab.OnModOptionChange"/>

Penumbra/Import/TexToolsImporter.ModPack.cs

@@ -205,7 +205,7 @@ private DirectoryInfo ImportExtendedV2ModPack(ZipArchive extractedModPack, strin
                         {
                             var option = group.OptionList[idx];
                             _currentOptionName = option.Name;
-                            options.Insert(idx, MultiSubMod.CreateForSaving(option.Name, option.Description, ModPriority.Default));
+                            options.Insert(idx, MultiSubMod.WithoutGroup(option.Name, option.Description, ModPriority.Default));
                             if (option.IsChecked)
                                 defaultSettings = Setting.Single(idx);
                         }

Penumbra/Mods/Editor/DuplicateManager.cs

@@ -60,7 +60,7 @@ public void Clear()
 
     private void HandleDuplicate(Mod mod, FullPath duplicate, FullPath remaining, bool useModManager)
     {
-        ModEditor.ApplyToAllOptions(mod, HandleSubMod);
+        ModEditor.ApplyToAllContainers(mod, HandleSubMod);
 
         try
         {
@@ -73,7 +73,7 @@ private void HandleDuplicate(Mod mod, FullPath duplicate, FullPath remaining, bo
 
         return;
 
-        void HandleSubMod(IModDataContainer subMod, int groupIdx, int optionIdx)
+        void HandleSubMod(IModDataContainer subMod)
         {
             var changes = false;
             var dict = subMod.Files.ToDictionary(kvp => kvp.Key,
@@ -82,14 +82,9 @@ void HandleSubMod(IModDataContainer subMod, int groupIdx, int optionIdx)
                 return;
 
             if (useModManager)
-            {
-                modManager.OptionEditor.OptionSetFiles(mod, groupIdx, optionIdx, dict, SaveType.ImmediateSync);
-            }
+                modManager.OptionEditor.SetFiles(subMod, dict, SaveType.ImmediateSync);
             else
-            {
-                subMod.Files = dict;
-                saveService.ImmediateSaveSync(new ModSaveGroup(mod, groupIdx, config.ReplaceNonAsciiOnImport));
-            }
+                saveService.ImmediateSaveSync(new ModSaveGroup(mod.ModPath, subMod, config.ReplaceNonAsciiOnImport));
         }
     }
 

Penumbra/Mods/Editor/ModEditor.cs

@@ -29,8 +29,8 @@ public class ModEditor(
     public int  GroupIdx { get; private set; }
     public int  DataIdx  { get; private set; }
 
-    public IModGroup?         Group          { get; private set; }
-    public IModDataContainer? Option         { get; private set; }
+    public IModGroup?         Group  { get; private set; }
+    public IModDataContainer? Option { get; private set; }
 
     public void LoadMod(Mod mod)
         => LoadMod(mod, -1, 0);
@@ -63,10 +63,10 @@ private void LoadOption(int groupIdx, int dataIdx, bool message)
         {
             if (groupIdx == -1 && dataIdx == 0)
             {
-                Group          = null;
-                Option         = Mod.Default;
-                GroupIdx       = groupIdx;
-                DataIdx        = dataIdx;
+                Group    = null;
+                Option   = Mod.Default;
+                GroupIdx = groupIdx;
+                DataIdx  = dataIdx;
                 return;
             }
 
@@ -75,18 +75,18 @@ private void LoadOption(int groupIdx, int dataIdx, bool message)
                 Group = Mod.Groups[groupIdx];
                 if (dataIdx >= 0 && dataIdx < Group.DataContainers.Count)
                 {
-                    Option         = Group.DataContainers[dataIdx];
-                    GroupIdx       = groupIdx;
-                    DataIdx        = dataIdx;
+                    Option   = Group.DataContainers[dataIdx];
+                    GroupIdx = groupIdx;
+                    DataIdx  = dataIdx;
                     return;
                 }
             }
         }
 
-        Group          = null;
-        Option         = Mod?.Default;
-        GroupIdx       = -1;
-        DataIdx        = 0;
+        Group    = null;
+        Option   = Mod?.Default;
+        GroupIdx = -1;
+        DataIdx  = 0;
         if (message)
             Penumbra.Log.Error($"Loading invalid option {groupIdx} {dataIdx} for Mod {Mod?.Name ?? "Unknown"}.");
     }
@@ -105,23 +105,11 @@ public void Dispose()
         => Clear();
 
     /// <summary> Apply a option action to all available option in a mod, including the default option. </summary>
-    public static void ApplyToAllOptions(Mod mod, Action<IModDataContainer, int, int> action)
+    public static void ApplyToAllContainers(Mod mod, Action<IModDataContainer> action)
     {
-        action(mod.Default, -1, 0);
-        foreach (var (group, groupIdx) in mod.Groups.WithIndex())
-        {
-            switch (group)
-            {
-                case SingleModGroup single:
-                    for (var optionIdx = 0; optionIdx < single.OptionData.Count; ++optionIdx)
-                        action(single.OptionData[optionIdx], groupIdx, optionIdx);
-                    break;
-                case MultiModGroup multi:
-                    for (var optionIdx = 0; optionIdx < multi.OptionData.Count; ++optionIdx)
-                        action(multi.OptionData[optionIdx], groupIdx, optionIdx);
-                    break;
-            }
-        }
+        action(mod.Default);
+        foreach (var container in mod.Groups.SelectMany(g => g.DataContainers))
+            action(container);
     }
 
     // Does not delete the base directory itself even if it is completely empty at the end.

Penumbra/Mods/Editor/ModFileEditor.cs

@@ -24,8 +24,7 @@ public int Apply(Mod mod, IModDataContainer option)
                 num += dict.TryAdd(path.Item2, file.File) ? 0 : 1;
         }
 
-        var (groupIdx, dataIdx) = option.GetDataIndices();
-        modManager.OptionEditor.OptionSetFiles(mod, groupIdx, dataIdx, dict);
+        modManager.OptionEditor.SetFiles(option, dict);
         files.UpdatePaths(mod, option);
         Changes = false;
         return num;
@@ -40,15 +39,15 @@ public void Revert(Mod mod, IModDataContainer option)
     /// <summary> Remove all path redirections where the pointed-to file does not exist. </summary>
     public void RemoveMissingPaths(Mod mod, IModDataContainer option)
     {
-        void HandleSubMod(IModDataContainer subMod, int groupIdx, int optionIdx)
+        void HandleSubMod(IModDataContainer subMod)
         {
             var newDict = subMod.Files.Where(kvp => CheckAgainstMissing(mod, subMod, kvp.Value, kvp.Key, subMod == option))
                 .ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
             if (newDict.Count != subMod.Files.Count)
-                modManager.OptionEditor.OptionSetFiles(mod, groupIdx, optionIdx, newDict);
+                modManager.OptionEditor.SetFiles(subMod, newDict);
         }
 
-        ModEditor.ApplyToAllOptions(mod, HandleSubMod);
+        ModEditor.ApplyToAllContainers(mod, HandleSubMod);
         files.ClearMissingFiles();
     }