Note that you can disable this message in “Settings”->”Configure Settings” menu and launch the Script Merger manually with “Run Script Merger” button. Pressing “Yes” launches the Script Merger.
Here’s a screenshot of an updated GUI for the manager: With 0.3BETA update the guide just got even simpler: In my previous post about Mod Manager I wrote a guide on how to use it for installing mods one-by-one. UI improvements, bug fixes and new features in Witcher 3 Mod Installer/Manager 0.3BETA update by stefan3372.