RunUAT BuildCookRun deletes AutomationScripts folder

I use 4.9. This is my shell script which I use in Jenkins CI tool:
For Android:
/Users/Shared/UnrealEngine/4.9/Engine/Build/BatchFiles/RunUAT.command BuildCookRun -rocket -nocompile -nocompileeditor -installed -nop4 -project=“$projectfile” -cook -stage -archive -archivedirectory=“$outputdir” -package -clientconfig=$buildtype -ue4exe=UE4Editor -clean -compressed -CookAll -pak -prereqs -distribution -nodebuginfo -targetplatform=Android -build -utf8output

For iOS

/Users/Shared/UnrealEngine/4.9/Engine/Build/BatchFiles/RunUAT.command BuildCookRun -rocket -nocompile -nocompileeditor -installed -nop4 -project=“$projectfile” -cook -stage -archive -archivedirectory=“$outputdir” -package -clientconfig=$buildtype -ue4exe=UE4Editor -clean -compressed -CookAll -pak -prereqs -distribution -nodebuginfo -targetplatform=IOS -build -utf8output