Stellaris Mod Manager
The "Stellaris Mod Manager" tool by Wojciech Krysiak is an invaluable tool to anyone that uses more than a handful of mods in Stellaris.
As the number of mods for Stellaris increases - and it's now in the region of 10,000, according to the Steam Workshop - so, too, does the opportunity for conflict. The Stellaris Module Manager will detect conflicts between mods in your load-out based on whether or not they both modify the same vanilla file. If they do, it identifies which file is conflicting and offers the ability to merge the changes, in the hopes that the mods become compatible.