Fixes regarding collection settings, change self-conflict behaviour by iterating through options instead of through files, button to clean up collection settings.

Penumbra/Meta/MetaManager.cs

@@ -44,7 +44,7 @@ namespace Penumbra.Meta
 
         private readonly MetaDefaults                     _default;
         private readonly DirectoryInfo                    _dir;
-        private readonly ResidentResources           _resourceManagement;
+        private readonly ResidentResources                _resourceManagement;
         private readonly Dictionary< GamePath, FileInfo > _resolvedFiles;
 
         private readonly Dictionary< MetaManipulation, Mod.Mod > _currentManipulations = new();
@@ -53,6 +53,10 @@ namespace Penumbra.Meta
         public IEnumerable< (MetaManipulation, Mod.Mod) > Manipulations
             => _currentManipulations.Select( kvp => ( kvp.Key, kvp.Value ) );
 
+        public IEnumerable< (GamePath, FileInfo) > Files
+            => _currentFiles.Where( kvp => kvp.Value.CurrentFile != null )
+               .Select( kvp => ( kvp.Key, kvp.Value.CurrentFile! ) );
+
         public int Count
             => _currentManipulations.Count;
 

Penumbra/Mods/ModCollection.cs

@@ -109,7 +109,7 @@ namespace Penumbra.Mods
             }
         }
 
-        public void UpdateSettings()
+        public void UpdateSettings( bool forceSave )
         {
             if( Cache == null )
             {
@@ -122,7 +122,7 @@ namespace Penumbra.Mods
                 changes |= mod.FixSettings();
             }
 
-            if( changes )
+            if( forceSave || changes )
             {
                 Save();
             }
@@ -133,7 +133,7 @@ namespace Penumbra.Mods
             PluginLog.Debug( "Recalculating effective file list for {CollectionName} [{WithMetaManipulations}] [{IsActiveCollection}]", Name,
                 withMetaManipulations, activeCollection );
             Cache ??= new ModCollectionCache( Name, modDir );
-            UpdateSettings();
+            UpdateSettings( false );
             Cache.CalculateEffectiveFileList();
             if( withMetaManipulations )
             {

Penumbra/Mods/ModCollectionCache.cs

@@ -1,11 +1,16 @@
-using System;
+using System.Collections;
 using System.Collections.Generic;
+using System.ComponentModel;
+using System.Diagnostics;
 using System.IO;
 using System.Linq;
-using Lumina.Data.Parsing;
+using System.Runtime.InteropServices;
+using Dalamud.Logging;
 using Penumbra.GameData.Util;
 using Penumbra.Meta;
 using Penumbra.Mod;
+using Penumbra.Structs;
+using Penumbra.Util;
 
 namespace Penumbra.Mods
 {
@@ -13,42 +18,206 @@ namespace Penumbra.Mods
     // It will only be setup if a collection gets activated in any way.
     public class ModCollectionCache
     {
+        // Shared caches to avoid allocations.
+        private static readonly BitArray                        FileSeen        = new( 256 );
+        private static readonly Dictionary< GamePath, Mod.Mod > RegisteredFiles = new( 256 );
+
         public readonly Dictionary< string, Mod.Mod > AvailableMods = new();
 
         public readonly Dictionary< GamePath, FileInfo > ResolvedFiles = new();
         public readonly Dictionary< GamePath, GamePath > SwappedFiles  = new();
+        public readonly HashSet< FileInfo >              MissingFiles  = new();
         public readonly MetaManager                      MetaManipulations;
 
         public ModCollectionCache( string collectionName, DirectoryInfo tempDir )
             => MetaManipulations = new MetaManager( collectionName, ResolvedFiles, tempDir );
 
-        private void AddFiles( Dictionary< GamePath, Mod.Mod > registeredFiles, Mod.Mod mod )
+        private static void ResetFileSeen( int size )
         {
-            foreach( var file in mod.Data.Resources.ModFiles )
+            if( size < FileSeen.Length )
             {
-                var gamePaths = mod.GetFiles( file );
+                FileSeen.Length = size;
-                foreach( var gamePath in gamePaths )
+                FileSeen.SetAll( false );
+            }
+            else
+            {
+                FileSeen.SetAll( false );
+                FileSeen.Length = size;
+            }
+        }
+
+        public void CalculateEffectiveFileList()
+        {
+            ResolvedFiles.Clear();
+            SwappedFiles.Clear();
+            MissingFiles.Clear();
+            RegisteredFiles.Clear();
+
+            foreach( var mod in AvailableMods.Values
+               .Where( m => m.Settings.Enabled )
+               .OrderByDescending( m => m.Settings.Priority ) )
+            {
+                mod.Cache.ClearFileConflicts();
+                AddFiles( mod );
+                AddSwaps( mod );
+            }
+
+            AddMetaFiles();
+        }
+
+
+        private void AddFiles( Mod.Mod mod )
+        {
+            ResetFileSeen( mod.Data.Resources.ModFiles.Count );
+            // Iterate in reverse so that later groups take precedence before earlier ones.
+            foreach( var group in mod.Data.Meta.Groups.Values.Reverse() )
+            {
+                switch( group.SelectionType )
                 {
-                    if( !registeredFiles.TryGetValue( gamePath, out var oldMod ) )
+                    case SelectType.Single:
+                        AddFilesForSingle( group, mod );
+                        break;
+                    case SelectType.Multi:
+                        AddFilesForMulti( group, mod );
+                        break;
+                    default: throw new InvalidEnumArgumentException();
+                }
+            }
+
+            AddRemainingFiles( mod );
+        }
+
+        private void AddFile( Mod.Mod mod, GamePath gamePath, FileInfo file )
+        {
+            if( !RegisteredFiles.TryGetValue( gamePath, out var oldMod ) )
+            {
+                RegisteredFiles.Add( gamePath, mod );
+                ResolvedFiles[ gamePath ] = file;
+            }
+            else
+            {
+                mod.Cache.AddConflict( oldMod, gamePath );
+            }
+        }
+
+        private void AddMissingFile( FileInfo file )
+        {
+            switch( file.Extension.ToLowerInvariant() )
+            {
+                case ".meta":
+                case ".rgsp":
+                    return;
+                default:
+                    MissingFiles.Add( file );
+                    return;
+            }
+        }
+
+        private void AddPathsForOption( Option option, Mod.Mod mod, bool enabled )
+        {
+            foreach( var (file, paths) in option.OptionFiles )
+            {
+                var fullPath = Path.Combine( mod.Data.BasePath.FullName, file );
+                var idx      = mod.Data.Resources.ModFiles.IndexOf( f => f.FullName == fullPath );
+                if( idx < 0 )
+                {
+                    AddMissingFile( new FileInfo( fullPath ) );
+                    continue;
+                }
+
+                var registeredFile = mod.Data.Resources.ModFiles[ idx ];
+                registeredFile.Refresh();
+                if( !registeredFile.Exists )
+                {
+                    AddMissingFile( registeredFile );
+                    continue;
+                }
+
+                FileSeen.Set( idx, true );
+                if( enabled )
+                {
+                    foreach( var path in paths )
                     {
-                        registeredFiles.Add( gamePath, mod );
+                        AddFile( mod, path, registeredFile );
-                        ResolvedFiles[ gamePath ] = file;
-                    }
-                    else
-                    {
-                        mod.Cache.AddConflict( oldMod, gamePath );
                     }
                 }
             }
         }
 
-        private void AddSwaps( Dictionary< GamePath, Mod.Mod > registeredFiles, Mod.Mod mod )
+        private void AddFilesForSingle( OptionGroup singleGroup, Mod.Mod mod )
+        {
+            Debug.Assert( singleGroup.SelectionType == SelectType.Single );
+
+            if( !mod.Settings.Settings.TryGetValue( singleGroup.GroupName, out var setting ) )
+            {
+                setting = 0;
+            }
+
+            for( var i = 0; i < singleGroup.Options.Count; ++i )
+            {
+                AddPathsForOption( singleGroup.Options[ i ], mod, setting == i );
+            }
+        }
+
+        private void AddFilesForMulti( OptionGroup multiGroup, Mod.Mod mod )
+        {
+            Debug.Assert( multiGroup.SelectionType == SelectType.Multi );
+
+            if( !mod.Settings.Settings.TryGetValue( multiGroup.GroupName, out var setting ) )
+            {
+                return;
+            }
+
+            // Also iterate options in reverse so that later options take precedence before earlier ones.
+            for( var i = multiGroup.Options.Count - 1; i >= 0; --i )
+            {
+                AddPathsForOption( multiGroup.Options[ i ], mod, ( setting & ( 1 << i ) ) != 0 );
+            }
+        }
+
+        private void AddRemainingFiles( Mod.Mod mod )
+        {
+            for( var i = 0; i < mod.Data.Resources.ModFiles.Count; ++i )
+            {
+                if( FileSeen.Get( i ) )
+                {
+                    continue;
+                }
+
+                var file = mod.Data.Resources.ModFiles[ i ];
+                file.Refresh();
+                if( file.Exists )
+                {
+                    AddFile( mod, new GamePath( file, mod.Data.BasePath ), file );
+                }
+                else
+                {
+                    MissingFiles.Add( file ); 
+                }
+            }
+        }
+
+        private void AddMetaFiles()
+        {
+            foreach( var (gamePath, file) in MetaManipulations.Files )
+            {
+                if( RegisteredFiles.TryGetValue( gamePath, out var mod ) )
+                {
+                    PluginLog.Warning(
+                        $"The meta manipulation file {gamePath} was already completely replaced by {mod.Data.Meta.Name}. This is probably a mistake. Using the custom file {file.FullName}." );
+                }
+
+                ResolvedFiles[ gamePath ] = file;
+            }
+        }
+
+        private void AddSwaps( Mod.Mod mod )
         {
             foreach( var swap in mod.Data.Meta.FileSwaps )
             {
-                if( !registeredFiles.TryGetValue( swap.Key, out var oldMod ) )
+                if( !RegisteredFiles.TryGetValue( swap.Key, out var oldMod ) )
                 {
-                    registeredFiles.Add( swap.Key, mod );
+                    RegisteredFiles.Add( swap.Key, mod );
                     SwappedFiles.Add( swap.Key, swap.Value );
                 }
                 else
@@ -86,22 +255,6 @@ namespace Penumbra.Mods
             MetaManipulations.WriteNewFiles();
         }
 
-        public void CalculateEffectiveFileList()
-        {
-            ResolvedFiles.Clear();
-            SwappedFiles.Clear();
-
-            var registeredFiles = new Dictionary< GamePath, Mod.Mod >();
-            foreach( var mod in AvailableMods.Values
-               .Where( m => m.Settings.Enabled )
-               .OrderByDescending( m => m.Settings.Priority ) )
-            {
-                mod.Cache.ClearFileConflicts();
-                AddFiles( registeredFiles, mod );
-                AddSwaps( registeredFiles, mod );
-            }
-        }
-
         public void RemoveMod( DirectoryInfo basePath )
         {
             if( AvailableMods.TryGetValue( basePath.Name, out var mod ) )
@@ -121,7 +274,7 @@ namespace Penumbra.Mods
         private class PriorityComparer : IComparer< Mod.Mod >
         {
             public int Compare( Mod.Mod? x, Mod.Mod? y )
-                => (x?.Settings.Priority ?? 0).CompareTo( y?.Settings.Priority ?? 0 );
+                => ( x?.Settings.Priority ?? 0 ).CompareTo( y?.Settings.Priority ?? 0 );
         }
 
         private static readonly PriorityComparer Comparer = new();

Penumbra/Structs/GroupInformation.cs

@@ -43,12 +43,14 @@ namespace Penumbra.Structs
 
         private bool ApplySingleGroupFiles( RelPath relPath, int selection, HashSet< GamePath > paths )
         {
+            // Selection contains the path, merge all GamePaths for this config.
             if( Options[ selection ].OptionFiles.TryGetValue( relPath, out var groupPaths ) )
             {
                 paths.UnionWith( groupPaths );
                 return true;
             }
 
+            // If the group contains the file in another selection, return true to skip it for default files.
             for( var i = 0; i < Options.Count; ++i )
             {
                 if( i == selection )

Penumbra/UI/Custom/ImGuiUtil.cs

@@ -1,3 +1,4 @@
+using System.Numerics;
 using System.Security.Cryptography.X509Certificates;
 using System.Windows.Forms;
 using Dalamud.Interface;
@@ -53,6 +54,15 @@ namespace Penumbra.UI.Custom
         }
     }
 
+    public static partial class ImGuiCustom
+    {
+        public static bool DisableButton( string label, bool condition )
+        {
+            using var alpha = ImGuiRaii.PushStyle( ImGuiStyleVar.Alpha, 0.5f, !condition );
+            return ImGui.Button( label ) && condition;
+        }
+    }
+
     public static partial class ImGuiCustom
     {
         public static void PrintIcon( FontAwesomeIcon icon )

Penumbra/UI/MenuTabs/TabCollections.cs

@@ -87,13 +87,25 @@ namespace Penumbra.UI
             {
                 if( _manager.Collections.AddCollection( _newCollectionName, settings ) )
                 {
-                    _manager.Collections.SetCurrentCollection( _manager.Collections.Collections[ _newCollectionName ] );
                     UpdateNames();
+                    SetCurrentCollection( _manager.Collections.Collections[_newCollectionName], true );
                 }
 
                 _newCollectionName = string.Empty;
             }
 
+            private void DrawCleanCollectionButton()
+            {
+                if( ImGui.Button( "Clean Settings" ) )
+                {
+                    var changes = ModFunctions.CleanUpCollection( _manager.Collections.CurrentCollection.Settings,
+                        _manager.BasePath.EnumerateDirectories() );
+                    _manager.Collections.CurrentCollection.UpdateSettings( forceSave: changes );
+                }
+
+                ImGuiCustom.HoverTooltip( "Remove all stored settings for mods not currently available and fix invalid settings.\nUse at own risk." );
+            }
+
             private void DrawNewCollectionInput()
             {
                 ImGui.InputTextWithHint( "##New Collection", "New Collection", ref _newCollectionName, 64 );
@@ -113,26 +125,31 @@ namespace Penumbra.UI
 
                 style.Pop();
 
-                if( _manager.Collections.Collections.Count      > 1
+                var deleteCondition = _manager.Collections.Collections.Count > 1
-                 && _manager.Collections.CurrentCollection.Name != ModCollection.DefaultCollection )
+                 && _manager.Collections.CurrentCollection.Name              != ModCollection.DefaultCollection;
+                ImGui.SameLine();
+                if( ImGuiCustom.DisableButton( "Delete Current Collection",  deleteCondition) )
+                {
+                    _manager.Collections.RemoveCollection( _manager.Collections.CurrentCollection.Name );
+                    SetCurrentCollection( _manager.Collections.CurrentCollection, true );
+                    UpdateNames();
+                }
+
+                if( Penumbra.Config.ShowAdvanced )
                 {
                     ImGui.SameLine();
-                    if( ImGui.Button( "Delete Current Collection" ) )
+                    DrawCleanCollectionButton();
-                    {
-                        _manager.Collections.RemoveCollection( _manager.Collections.CurrentCollection.Name );
-                        UpdateNames();
-                    }
                 }
             }
 
-            private void SetCurrentCollection( int idx )
+            private void SetCurrentCollection( int idx, bool force )
             {
-                if( idx == _currentCollectionIndex )
+                if( !force && idx == _currentCollectionIndex )
                 {
                     return;
                 }
 
-                _manager.Collections.SetCurrentCollection( _collections[ idx + 1 ] );
+                _manager.Collections.SetCurrentCollection( _collections[idx + 1] );
                 _currentCollectionIndex = idx;
                 _selector.Cache.TriggerListReset();
                 if( _selector.Mod != null )
@@ -141,12 +158,12 @@ namespace Penumbra.UI
                 }
             }
 
-            public void SetCurrentCollection( ModCollection collection )
+            public void SetCurrentCollection( ModCollection collection, bool force = false )
             {
                 var idx = Array.IndexOf( _collections, collection ) - 1;
                 if( idx >= 0 )
                 {
-                    SetCurrentCollection( idx );
+                    SetCurrentCollection( idx, force );
                 }
             }
 
@@ -159,7 +176,7 @@ namespace Penumbra.UI
 
                 if( combo )
                 {
-                    SetCurrentCollection( index );
+                    SetCurrentCollection( index, false );
                 }
             }
 
@@ -205,18 +222,14 @@ namespace Penumbra.UI
             {
                 ImGui.InputTextWithHint( "##New Character", "New Character Name", ref _newCharacterName, 32 );
 
-                using var style = ImGuiRaii.PushStyle( ImGuiStyleVar.Alpha, 0.5f, _newCharacterName.Length == 0 );
-
                 ImGui.SameLine();
-                if( ImGui.Button( "Create New Character Collection" ) && _newCharacterName.Length > 0 )
+                if( ImGuiCustom.DisableButton( "Create New Character Collection", _newCharacterName.Length > 0 ))
                 {
                     _manager.Collections.CreateCharacterCollection( _newCharacterName );
                     _currentCharacterIndices[ _newCharacterName ] = 0;
                     _newCharacterName                             = string.Empty;
                 }
 
-                style.Pop();
-
                 ImGuiCustom.HoverTooltip(
                     "A character collection will be used whenever you manually redraw a character with the Name you have set up.\n"
                   + "If you enable automatic character redraws in the Settings tab, penumbra will try to use Character collections for corresponding characters automatically.\n" );

Penumbra/UI/MenuTabs/TabDebug.cs

@@ -342,6 +342,34 @@ namespace Penumbra.UI
             }
         }
 
+        private void DrawDebugTabMissingFiles()
+        {
+            if( !ImGui.CollapsingHeader( "Missing Files##Debug" ) )
+            {
+                return;
+            }
+
+            var manager = Service<ModManager>.Get();
+            var cache   = manager.Collections.CurrentCollection.Cache;
+            if( cache == null || !ImGui.BeginTable( "##MissingFilesDebugList", 1, ImGuiTableFlags.RowBg, -Vector2.UnitX))
+            {
+                return;
+            }
+
+            using var raii = ImGuiRaii.DeferredEnd( ImGui.EndTable );
+
+            foreach( var file in cache.MissingFiles )
+            {
+                ImGui.TableNextRow();
+                ImGui.TableNextColumn();
+                if( ImGui.Selectable( file.FullName ) )
+                {
+                    ImGui.SetClipboardText( file.FullName );
+                }
+                ImGuiCustom.HoverTooltip( "Click to copy to clipboard." );
+            }
+        }
+
         private void DrawDebugTab()
         {
             if( !ImGui.BeginTabItem( "Debug Tab" ) )
@@ -353,6 +381,8 @@ namespace Penumbra.UI
 
             DrawDebugTabGeneral();
             ImGui.NewLine();
+            DrawDebugTabMissingFiles();
+            ImGui.NewLine();
             DrawDebugTabRedraw();
             ImGui.NewLine();
             DrawDebugTabPlayers();

Penumbra/Util/ArrayExtensions.cs

@@ -72,5 +72,16 @@ namespace Penumbra.Util
 
             array.Swap( idx1, idx2 );
         }
+
+        public static int IndexOf< T >( this IList< T > array, Func< T, bool > predicate )
+        {
+            for( var i = 0; i < array.Count; ++i )
+            {
+                if( predicate.Invoke( array[ i ] ) )
+                    return i;
+            }
+
+            return -1;
+        }
     }
 }