Fix some caching issues.

Penumbra/Collections/Cache/CollectionCacheManager.cs

@@ -51,6 +51,8 @@ public class CollectionCacheManager : IDisposable
         _communicator.ModOptionChanged.Subscribe(OnModOptionChange, -100);
         _communicator.ModSettingChanged.Subscribe(OnModSettingChange);
         _communicator.CollectionInheritanceChanged.Subscribe(OnCollectionInheritanceChange);
+        _communicator.ModDiscoveryStarted.Subscribe(OnModDiscoveryStarted);
+        _communicator.ModDiscoveryFinished.Subscribe(OnModDiscoveryFinished, -100);
 
         if (!MetaFileManager.CharacterUtility.Ready)
             MetaFileManager.CharacterUtility.LoadingFinished += IncrementCounters;
@@ -308,4 +310,20 @@ public class CollectionCacheManager : IDisposable
         Penumbra.Log.Debug($"Creating {tasks.Length} necessary caches.");
         Task.WaitAll(tasks);
     }
+
+    private void OnModDiscoveryStarted()
+    {
+        foreach (var collection in Active)
+        {
+            collection._cache!.ResolvedFiles.Clear();
+            collection._cache!.Meta.Reset();
+            collection._cache!._conflicts.Clear();
+        }
+    }
+
+    private void OnModDiscoveryFinished()
+    {
+        var tasks = Active.Select(c => Task.Run(() => CalculateEffectiveFileListInternal(c))).ToArray();
+        Task.WaitAll(tasks);
+    }
 }

Penumbra/Mods/Manager/ModCacheManager.cs

@@ -168,10 +168,10 @@ public class ModCacheManager : IDisposable
         => mod.TotalFileCount = mod.AllSubMods.Sum(s => s.Files.Count);
 
     private static void UpdateSwapCount(Mod mod)
-        => mod.TotalFileCount = mod.AllSubMods.Sum(s => s.FileSwaps.Count);
+        => mod.TotalSwapCount = mod.AllSubMods.Sum(s => s.FileSwaps.Count);
 
     private static void UpdateMetaCount(Mod mod)
-        => mod.TotalFileCount = mod.AllSubMods.Sum(s => s.Manipulations.Count);
+        => mod.TotalManipulations = mod.AllSubMods.Sum(s => s.Manipulations.Count);
 
     private static void UpdateHasOptions(Mod mod)
         => mod.HasOptions = mod.Groups.Any(o => o.IsOption);

Penumbra/Mods/Manager/ModManager.cs

@@ -29,7 +29,7 @@ public enum ModPathChangeType
     StartingReload,
 }
 
-public sealed class ModManager : ModStorage
+public sealed class ModManager : ModStorage, IDisposable
 {
     private readonly Configuration       _config;
     private readonly CommunicatorService _communicator;
@@ -50,6 +50,7 @@ public sealed class ModManager : ModStorage
         OptionEditor  = optionEditor;
         Creator    = creator;
         SetBaseDirectory(config.ModDirectory, true);
+        _communicator.ModPathChanged.Subscribe(OnModPathChange);
         DiscoverMods();
     }
 
@@ -66,7 +67,7 @@ public sealed class ModManager : ModStorage
     public void DiscoverMods()
     {
         _communicator.ModDiscoveryStarted.Invoke();
-        NewMods.Clear();
+        ClearNewMods();
         Mods.Clear();
         BasePath.Refresh();
 
@@ -244,10 +245,10 @@ public sealed class ModManager : ModStorage
         switch (type)
         {
             case ModPathChangeType.Added: 
-                NewMods.Add(mod);
+                SetNew(mod);
                 break;
             case ModPathChangeType.Deleted:
-                NewMods.Remove(mod);
+                SetKnown(mod);
                 break;
             case ModPathChangeType.Moved:
                 if (oldDirectory != null && newDirectory != null)
@@ -258,7 +259,7 @@ public sealed class ModManager : ModStorage
     }
 
     public void Dispose()
-    { }
+        => _communicator.ModPathChanged.Unsubscribe(OnModPathChange);
 
     /// <summary>
     /// Set the mod base directory.

Penumbra/Mods/Manager/ModOptionEditor.cs

@@ -314,7 +314,7 @@ public class ModOptionEditor
             return;
 
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.PrepareChange, mod, groupIdx, optionIdx, -1);
-        subMod.ManipulationData = manipulations;
+        subMod.ManipulationData.SetTo(manipulations);
         _saveService.QueueSave(new ModSaveGroup(mod, groupIdx));
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.OptionMetaChanged, mod, groupIdx, optionIdx, -1);
     }
@@ -327,7 +327,7 @@ public class ModOptionEditor
             return;
 
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.PrepareChange, mod, groupIdx, optionIdx, -1);
-        subMod.FileData = replacements;
+        subMod.FileData.SetTo(replacements);
         _saveService.QueueSave(new ModSaveGroup(mod, groupIdx));
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.OptionFilesChanged, mod, groupIdx, optionIdx, -1);
     }
@@ -353,7 +353,7 @@ public class ModOptionEditor
             return;
 
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.PrepareChange, mod, groupIdx, optionIdx, -1);
-        subMod.FileSwapData = swaps;
+        subMod.FileSwapData.SetTo(swaps);
         _saveService.QueueSave(new ModSaveGroup(mod, groupIdx));
         _communicator.ModOptionChanged.Invoke(ModOptionChangeType.OptionSwapsChanged, mod, groupIdx, optionIdx, -1);
     }

Penumbra/Mods/Manager/ModStorage.cs

@@ -53,14 +53,17 @@ public class ModStorage : IReadOnlyList<Mod>
     /// Mods are removed when they are deleted or when they are toggled in any collection.
     /// Also gets cleared on mod rediscovery.
     /// </summary>
-    protected readonly HashSet<Mod> NewMods = new();
+    private readonly HashSet<Mod> _newMods = new();
 
     public bool IsNew(Mod mod)
-        => NewMods.Contains(mod);
+        => _newMods.Contains(mod);
 
     public void SetNew(Mod mod)
-        => NewMods.Add(mod);
+        => _newMods.Add(mod);
 
     public void SetKnown(Mod mod)
-        => NewMods.Remove(mod);
+        => _newMods.Remove(mod);
+
+    public void ClearNewMods()
+        => _newMods.Clear();
 }

Penumbra/UI/AdvancedWindow/ModEditWindow.cs

@@ -414,7 +414,7 @@ public partial class ModEditWindow : Window, IDisposable
         if (ImGuiUtil.DrawDisabledButton("Revert Changes", Vector2.Zero, tt, setsEqual))
             _editor.SwapEditor.Revert(_editor.Option!);
 
-        var otherSwaps = _editor.Mod!.TotalSwapCount - _editor.SwapEditor.Swaps.Count;
+        var otherSwaps = _editor.Mod!.TotalSwapCount - _editor.Option!.FileSwaps.Count;
         if (otherSwaps > 0)
         {
             ImGui.SameLine();

Penumbra/Util/DictionaryExtensions.cs

@@ -6,7 +6,7 @@ namespace Penumbra.Util;
 
 public static class DictionaryExtensions
 {
-    // Returns whether two dictionaries contain equal keys and values.
+    /// <summary> Returns whether two dictionaries contain equal keys and values. </summary>
     public static bool SetEquals< TKey, TValue >( this IReadOnlyDictionary< TKey, TValue > lhs, IReadOnlyDictionary< TKey, TValue > rhs )
     {
         if( ReferenceEquals( lhs, rhs ) )
@@ -46,24 +46,32 @@ public static class DictionaryExtensions
         return true;
     }
 
-    // Set one dictionary to the other, deleting previous entries and ensuring capacity beforehand.
+    /// <summary> Set one dictionary to the other, deleting previous entries and ensuring capacity beforehand. </summary>
     public static void SetTo< TKey, TValue >( this Dictionary< TKey, TValue > lhs, IReadOnlyDictionary< TKey, TValue > rhs )
         where TKey : notnull
     {
         if( ReferenceEquals( lhs, rhs ) )
-        {
             return;
-        }
 
         lhs.Clear();
         lhs.EnsureCapacity( rhs.Count );
         foreach( var (key, value) in rhs )
-        {
             lhs.Add( key, value );
     }
+
+    /// <summary> Set one set to the other, deleting previous entries and ensuring capacity beforehand. </summary>
+    public static void SetTo<T>(this HashSet<T> lhs, IReadOnlySet<T> rhs)
+    {
+        if (ReferenceEquals(lhs, rhs))
+            return;
+
+        lhs.Clear();
+        lhs.EnsureCapacity(rhs.Count);
+        foreach (var value in rhs)
+            lhs.Add(value);
     }
 
-    // Add all entries from the other dictionary that would not overwrite current keys.
+    /// <summary> Add all entries from the other dictionary that would not overwrite current keys. </summary>
     public static void AddFrom< TKey, TValue >( this Dictionary< TKey, TValue > lhs, IReadOnlyDictionary< TKey, TValue > rhs )
         where TKey : notnull
     {