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.yml doesn't need to be prepared; it's already a ready-made file with settings.
Think of the "patcher" as a machine, and the .yml as a cartridge. You just need to download the patcher and put it in the root folder of the game, in the bin folder, and run it there. If you also have a .yml file in the root folder of the game, in the bin folder, it will offer you the option to patch the launcher (.Exe)** with it.
Then you need to write lists and form the internal structure of folders with files, but you've already created the folders with files. Essentially, you've already done the most important part; all that's left is to teach the executable to recognize what you've done and write a list of available creatures for it.
But how do you run the patcher itself? It has a .jar file extension. Windows sees it as an archive, but I don't see any .exe files inside to run it...