Shrill is a small program that takes mods in a certain form from a special folder and applies their changes to the base files. The base files are backed up first and each time to utility is launched creates the resulting files completely new from the (hopefully clean) backup files and the mods the user listed in the config file.
You can also have multiple different setups filled with different mods and switch between them by simply editing a single number and rerunning shrill.

It also allows modders to use a priority system which helps keeping the most important edit in case of conflict. For modders the only downside is that to use this utility they need to re-sort their mods into different files and rename a few.

Don't forget to run the utility (.luac file) after installing a new mod and adding it to a setup.