I have made a tool to improve mod management in kenshi:
For now, it helps to manage your load order with a better view.
but in a future, i will add possibilities to manage mods between Steam and kenshi folder (Copy and backup mods).
So an image is better than a long speech: Actually it's in beta but you can get it there if you want to test it.
https://www.dropbox.com/s/4pgk8okb9vv9q ... n.zip?dl=0
It should work with Steam and Non Steam version of the game, the only catch is that i can launch kenshi only through steam else the game start with an error "No available renderers found."