Hello.
I see i can add custom recipes to the machines (the syntax is in the github wiki), but i have no idea were to put the new files.
I HAVE to inject then inside the jar, or there is an easier way?
Could someone include that in the docs?

No need for mekanism to reinvent the wheel, it's all there already on the Minecraft Wiki. Here is just the folder structure.

As Oct0 said it just uses vanilla's data pack system which I am sure there is plenty of documentation on the internet for. I believe CrT also has a way to add json recipes (though I am not fully sure how that system works)