A free program for Windows, by DJ_Kovrik.

Witcher 3 Mod Merger is a simple tool created to help you avoid the “Mods limit” and assist you to merge your mods. It is used only if you encounter limit issues, and if it is not the case, then merging is not required anymore.

How can the Witcher 3 Mod Merger help you?

It deletes unnecessary raw images and unpacked files, unpacks files from mergeable mods, cooks and uncooks uncooked files, builds texture cache, generates metadata, and installs mod in your mod folder.

It is important to note that merging may take quite some time. Also, some mods can not be cooked or merged.