The recipe logic needs to be changed and refactored into modules.

The ShapedRecipe introduced a new NamespacedKey for recipes that should be used in 1.12 (https://hub.spigotmc.org/stash/projects/SPIGOT/repos/bukkit/commits/5ad2ecf658276b8aae336b0e5bfb894a5151b578#src/main/java/org/bukkit/inventory/ShapedRecipe.java)

Paper is now throwing issues: https://github.com/PaperMC/Paper/blob/master/Spigot-API-Patches/0076-Display-warning-on-deprecated-recipe-API.patch