diff --git a/CKAN/CmdLine/Action/Upgrade.cs b/CKAN/CmdLine/Action/Upgrade.cs
index 1882538f8d..843fbcd69d 100644
--- a/CKAN/CmdLine/Action/Upgrade.cs
+++ b/CKAN/CmdLine/Action/Upgrade.cs
@@ -1,4 +1,5 @@
 using System.Collections.Generic;
+using System.Linq;
 using System.Text.RegularExpressions;
 
 namespace CKAN.CmdLine
@@ -60,6 +61,14 @@ public int RunCommand(CKAN.KSP ksp, object raw_options)
             }
 
 
+            var auto_detected_modules = to_upgrade.Where(module => ksp.Registry.IsAutodetected(module.identifier)).ToList();
+            foreach (var module in auto_detected_modules.Select(mod => mod.identifier))
+            {
+                User.RaiseMessage("Cannot upgrade {0} as it was not installed by CKAN. \n Please remove manually before trying again", module);
+            }
+            //Exit if any are auto_detected
+            if (auto_detected_modules.Any()) return Exit.ERROR;   
+
             User.RaiseMessage("\nUpgrading modules...\n");
             // TODO: These instances all need to go.
             ModuleInstaller.GetInstance(ksp, User).Upgrade(to_upgrade,new NetAsyncDownloader(User));
diff --git a/CKAN/CmdLine/Main.cs b/CKAN/CmdLine/Main.cs
index 55331e6b9e..630aa3722d 100644
--- a/CKAN/CmdLine/Main.cs
+++ b/CKAN/CmdLine/Main.cs
@@ -155,6 +155,7 @@ public static int Main(string[] args)
                     return Available(manager.CurrentInstance, user);
 
                 case "install":
+                    Scan(manager.CurrentInstance);
                     return Install((InstallOptions)cmdline.options, manager.CurrentInstance, user);
 
                 case "scan":
@@ -170,6 +171,7 @@ public static int Main(string[] args)
                     return Remove((RemoveOptions)cmdline.options, manager.CurrentInstance, user);
 
                 case "upgrade":
+                    Scan(manager.CurrentInstance);
                     var upgrade = new Upgrade(user);
                     return upgrade.RunCommand(manager.CurrentInstance, cmdline.options);
 
diff --git a/CKAN/GUI/Util.cs b/CKAN/GUI/Util.cs
index fa6a92c204..4b6108c5e7 100644
--- a/CKAN/GUI/Util.cs
+++ b/CKAN/GUI/Util.cs
@@ -1,13 +1,14 @@
 using System;
-using System.Runtime.InteropServices;
-using System.Windows.Forms;
+
 
 namespace CKAN
 {
+    using System.Runtime.InteropServices;
+    using System.Windows.Forms;
 
     public static class Util
     {
-
+        
         public static bool IsLinux
         {
             get
@@ -75,12 +76,17 @@ public static void HideConsoleWindow()
                 ShowWindow(GetConsoleWindow(), 0);
             }
         }
+   }
+}
 
-
+namespace CKAN
+{
+    public static class UtilWithoutWinForm
+    {
         public static bool IsInstallable(this GUIMod mod)
         {
+
             return !(mod == null || mod.IsAutodetected || mod.IsIncompatible);
         }
-   }
-
+    }
 }