Added a whole lot of rudimentary comments, also importing selects the last imported mod if possible.

Penumbra/Mod/Mod.cs

@@ -4,6 +4,8 @@ using Penumbra.Util;
 
 namespace Penumbra.Mod
 {
+    // A complete Mod containing settings (i.e. dependent on a collection)
+    // and the resulting cache.
     public class Mod
     {
         public ModSettings Settings { get; }

Penumbra/Mod/ModCache.cs

@@ -5,6 +5,7 @@ using Penumbra.Util;
 
 namespace Penumbra.Mod
 {
+    // The ModCache contains volatile information dependent on all current settings in a collection.
     public class ModCache
     {
         public Dictionary< Mod, (List< GamePath > Files, List< MetaManipulation > Manipulations) > Conflicts { get; private set; } = new();

Penumbra/Mod/ModData.cs

@@ -3,6 +3,9 @@ using Dalamud.Plugin;
 
 namespace Penumbra.Mod
 {
+    // ModData contains all permanent information about a mod,
+    // and is independent of collections or settings.
+    // It only changes when the user actively changes the mod or their filesystem.
     public class ModData
     {
         public DirectoryInfo BasePath;

Penumbra/Mod/ModFunctions.cs

@@ -6,6 +6,7 @@ using Penumbra.Util;
 
 namespace Penumbra.Mod
 {
+    // Functions that do not really depend on only one component of a mod.
     public static class ModFunctions
     {
         public static bool CleanUpCollection( Dictionary< string, ModSettings > settings, IEnumerable< DirectoryInfo > modPaths )

Penumbra/Mod/ModMeta.cs

@@ -58,7 +58,6 @@ namespace Penumbra.Mod
             return true;
         }
 
-
         public static ModMeta? LoadFromFile( FileInfo filePath )
         {
             try

Penumbra/Mod/ModSettings.cs

@@ -5,6 +5,7 @@ using Penumbra.Structs;
 
 namespace Penumbra.Mod
 {
+    // Contains the settings for a given mod.
     public class ModSettings
     {
         public bool Enabled { get; set; }

Penumbra/Mod/NamedModSettings.cs

@@ -4,6 +4,9 @@ using Penumbra.Structs;
 
 namespace Penumbra.Mod
 {
+    // Contains settings with the option selections stored by names instead of index.
+    // This is meant to make them possibly more portable when we support importing collections from other users.
+    // Enabled does not exist, because disabled mods would not be exported in this way.
     public class NamedModSettings
     {
         public int Priority { get; set; }