Clean in update checkout

Author: ahoppen

utils/build-windows-toolchain.bat

@@ -109,7 +109,7 @@ set "args=%args% --skip-repository swift-integration-tests"
 set "args=%args% --skip-repository swift-stress-tester"
 set "args=%args% --skip-repository swift-xcode-playground-support"
 
-call "%SourceRoot%\swift\utils\update-checkout.cmd" %args% --clone --skip-history --reset-to-remote --github-comment "%ghprbCommentBody%"
+call "%SourceRoot%\swift\utils\update-checkout.cmd" %args% --reset-to-remote --clone --skip-history --clean --github-comment "%ghprbCommentBody%"
 
 goto :eof
 endlocal