diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73a860d2..57b4e65d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ to be a list of other profiles to be included in the install. This list should b
 * Any config files pointing to the download folder are remapped.
 * Refuse to run inside `downloads` folders (anti-virus watches these files too closely and it can cause VFS issues)
 * Refuse to run if MO2 is on the system installed in non-portable mode (otherwise broken installs may result) 
+* Config files that don't otherwise match a rule are inlined into the modlist
 
 #### Version 0.8.1 - 8/29/2019
 * Fixed a bug that was causing VFS temp folders not to be cleaned
diff --git a/Wabbajack.Common/Consts.cs b/Wabbajack.Common/Consts.cs
index dffea35f..e5819c4c 100644
--- a/Wabbajack.Common/Consts.cs
+++ b/Wabbajack.Common/Consts.cs
@@ -33,6 +33,7 @@ namespace Wabbajack.Common
         public static string NexusCacheDirectory = "nexus_link_cache";
 
         public static string WABBAJACK_INCLUDE = "WABBAJACK_INCLUDE";
+        public static string WABBAJACK_ALWAYS_ENABLE = "WABBAJACK_ALWAYS_ENABLE";
 
         public static string GAME_PATH_MAGIC_BACK = "{--||GAME_PATH_MAGIC_BACK||--}";
         public static string GAME_PATH_MAGIC_DOUBLE_BACK = "{--||GAME_PATH_MAGIC_DOUBLE_BACK||--}";
@@ -51,6 +52,5 @@ namespace Wabbajack.Common
         public static string HashCacheName = "Wabbajack.hash_cache";
 
         public static HashSet<string> GameESMs = new HashSet<string>() { "Skyrim.esm", "Update.esm", "Dawnguard.esm", "HearthFires.esm", "Dragonborn.esm" };
-        public static string WABBAJACK_ALWAYS_ENABLE = "WABBAJACK_ALWAYS_ENABLE";
     }
 }
diff --git a/Wabbajack/AppState.cs b/Wabbajack/AppState.cs
index 653a61af..ce513b9e 100644
--- a/Wabbajack/AppState.cs
+++ b/Wabbajack/AppState.cs
@@ -170,19 +170,6 @@ namespace Wabbajack
                 Environment.Exit(1);
             }
 
-            if (Directory.EnumerateDirectories(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "ModOrganizer"))
-                .Any(f => !f.EndsWith("\\cache")))
-            {
-                MessageBox.Show(
-                    "You seem to have a installed copy of Mod Organizer 2 on your system. Wabbajack requires that Mod Organizer 2 be run in `Portable` mode. " +
-                    "Unfortunately it is impossible to have both portable and non-portable versions of MO2 on the same system at the same time. Pleas uninstall Mod Organizer 2 " +
-                    "and use only portable (archive) versions with Wabbajack. If you get this message after uninstalling MO2, be sure to delete the folders in `AppData\\Local\\Mod Organizer`",
-                    "Cannot run with non-portable MO2 installed.",
-                    MessageBoxButton.OK,
-                    MessageBoxImage.Error);
-                Environment.Exit(2);
-            }
-
             _startTime = DateTime.Now;
             LogFile = Assembly.GetExecutingAssembly().Location + ".log";
 
diff --git a/Wabbajack/Compiler.cs b/Wabbajack/Compiler.cs
index 38d6a967..0a5ff4b1 100644
--- a/Wabbajack/Compiler.cs
+++ b/Wabbajack/Compiler.cs
@@ -12,6 +12,7 @@ using System.Security.Cryptography;
 using System.Text;
 using System.Text.RegularExpressions;
 using System.Web;
+using System.Windows.Documents;
 using CommonMark;
 using Wabbajack.Common;
 using static Wabbajack.NexusAPI;
@@ -585,10 +586,23 @@ namespace Wabbajack
 
                 PatchStockESMs(),
 
+                IncludeAllConfigs(),
+
                 DropAll()
             };
         }
 
+        private Func<RawSourceFile, Directive> IncludeAllConfigs()
+        {
+            return source =>
+            {
+                if (!Consts.ConfigFileExtensions.Contains(Path.GetExtension(source.Path))) return null;
+                var result = source.EvolveTo<InlineFile>();
+                result.SourceData = File.ReadAllBytes(source.AbsolutePath).ToBase64();
+                return result;
+            };
+        }
+
         private Func<RawSourceFile, Directive> PatchStockESMs()
         {
             return source =>