diff --git a/Wabbajack.Lib/CompilationSteps/IncludeVortexDeployment.cs b/Wabbajack.Lib/CompilationSteps/IncludeVortexDeployment.cs
index 2650a7c7..0269a07a 100644
--- a/Wabbajack.Lib/CompilationSteps/IncludeVortexDeployment.cs
+++ b/Wabbajack.Lib/CompilationSteps/IncludeVortexDeployment.cs
@@ -1,5 +1,8 @@
-using System.IO;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
 using System.Threading.Tasks;
+using Wabbajack.Common;
 
 namespace Wabbajack.Lib.CompilationSteps
 {
@@ -11,10 +14,21 @@ namespace Wabbajack.Lib.CompilationSteps
 
         public override async ValueTask<Directive> Run(RawSourceFile source)
         {
-            if (!source.Path.EndsWith("vortex.deployment.msgpack") &&
-                !source.Path.EndsWith("\\vortex.deployment.json") && Path.GetExtension(source.Path) != ".meta") return null;
+            var l = new List<string> {"vortex.deployment.msgpack", "vortex.deployment.json"};
+            if (!l.Any(a => source.Path.Contains(a))) return null;
             var inline = source.EvolveTo<InlineFile>();
             inline.SourceDataID = _compiler.IncludeFile(File.ReadAllBytes(source.AbsolutePath));
+            if (!source.Path.Contains("vortex.deployment.json"))
+                return inline;
+
+            var path = source.Path;
+            if (!path.StartsWith(Consts.GameFolderFilesDir))
+                return inline;
+
+            path = path.Substring(Consts.GameFolderFilesDir.Length + 1);
+            path = $"{Consts.ManualGameFilesDir}\\{path}";
+            inline.To = path;
+
             return inline;
         }
 
diff --git a/Wabbajack.Lib/VortexCompiler.cs b/Wabbajack.Lib/VortexCompiler.cs
index fdc5c16e..17e4642d 100644
--- a/Wabbajack.Lib/VortexCompiler.cs
+++ b/Wabbajack.Lib/VortexCompiler.cs
@@ -116,7 +116,7 @@ namespace Wabbajack.Lib
 
             UpdateTracker.NextStep("Finding Install Files");
             var vortexStagingFiles = Directory.EnumerateFiles(StagingFolder, "*", SearchOption.AllDirectories)
-                .Where(p => p.FileExists() && p != StagingMarkerName)
+                .Where(p => p.FileExists() && p != StagingMarkerName && !p.Contains(Consts.ManualGameFilesDir))
                 .Select(p => new RawSourceFile(VFS.Index.ByRootPath[p])
                     {Path = p.RelativeTo(StagingFolder)});
             
@@ -470,12 +470,12 @@ namespace Wabbajack.Lib
             return new List<ICompilationStep>
             {
                 new IncludePropertyFiles(this),
+                new IncludeVortexDeployment(this),
 
                 new IncludeSteamWorkshopItems(this, _steamGame),
                 _hasSteamWorkshopItems ? new IncludeRegex(this, "^steamWorkshopItem_\\d*\\.meta$") : null,
                 
                 new IgnoreDisabledVortexMods(this),
-                new IncludeVortexDeployment(this),
                 new IgnoreVortex(this),
                 new IgnoreRegex(this, $"^*{StagingMarkerName}$"),
 
diff --git a/Wabbajack.Lib/VortexInstaller.cs b/Wabbajack.Lib/VortexInstaller.cs
index 013ddef0..438bd44a 100644
--- a/Wabbajack.Lib/VortexInstaller.cs
+++ b/Wabbajack.Lib/VortexInstaller.cs
@@ -132,14 +132,14 @@ namespace Wabbajack.Lib
                 var dirInfo = new DirectoryInfo(dir);
                 dirInfo.GetDirectories("*", SearchOption.AllDirectories).Do(d =>
                 {
-                    var destPath = d.FullName.Replace(dir, gameFolder);
+                    var destPath = d.FullName.Replace(manualFilesDir, gameFolder);
                     Status($"Creating directory {destPath}");
                     Directory.CreateDirectory(destPath);
                 });
 
                 dirInfo.GetFiles("*", SearchOption.AllDirectories).Do(f =>
                 {
-                    var destPath = f.FullName.Replace(dir, gameFolder);
+                    var destPath = f.FullName.Replace(manualFilesDir, gameFolder);
                     Status($"Copying file {f.FullName} to {destPath}");
                     try
                     {
@@ -207,7 +207,7 @@ namespace Wabbajack.Lib
                     if (directive.To.EndsWith(".meta"))
                         return;
 
-                    Status($"Writing included file {directive.To}");
+                    Info($"Writing included file {directive.To}");
                     var outPath = Path.Combine(OutputFolder, directive.To);
                     if(File.Exists(outPath)) File.Delete(outPath);
                     File.WriteAllBytes(outPath, LoadBytesFromPath(directive.SourceDataID));