diff --git a/win_scripts/setup.bat b/win_scripts/setup.bat
index af77eb73..90b4dd33 100644
--- a/win_scripts/setup.bat
+++ b/win_scripts/setup.bat
@@ -7,13 +7,13 @@ mkdir C:\src\chromium\src\out\thorium &&
 
 echo "Copying Thorium source files over the Chromium tree..." &&
 
+copy ..\src\BUILD.gn C:\src\chromium\src\ &&
 copy ..\src\ash\* C:\src\chromium\src\ash &&
-copy ..\src\base\* C:\src\chromium\src\base &&
 copy ..\src\build\* C:\src\chromium\src\build &&
 copy ..\src\chrome\* C:\src\chromium\src\chrome &&
 copy ..\src\components\* C:\src\chromium\src\components &&
-copy ..\src\extensions\* C:\src\chromium\src\extensions &&
 copy ..\src\content\* C:\src\chromium\src\content &&
+copy ..\src\extensions\* C:\src\chromium\src\extensions &&
 copy ..\src\media\* C:\src\chromium\src\media &&
 copy ..\src\net\* C:\src\chromium\src\net &&
 copy ..\src\sandbox\* C:\src\chromium\src\sandbox &&
@@ -21,7 +21,7 @@ copy ..\src\third_party\* C:\src\chromium\src\third_party &&
 copy ..\src\tools\* C:\src\chromium\src\tools &&
 copy ..\src\ui\* C:\src\chromium\src\ui &&
 copy ..\src\v8\* C:\src\chromium\src\v8 &&
-copy ..\src\content_shell\* C:\src\chromium\src\out\thorium &&
+copy ..\src\thorium_shell\* C:\src\chromium\src\out\thorium &&
 copy ..\src\pak_src\bin\pak-win\* C:\src\chromium\src\out\thorium &&
 
 set NINJA_SUMMARIZE_BUILD=1 &&