In this update I made some things run a bit more efficiently.
The main bug that I fixed involved using the alter, where items that were not part of the crafting recipe would be consumed when added to the proper crafting recipe. Again this has been fixed.
I also added a config file in which you can enable and disable all the alter crafting recipes. This does not disable currently crafted items in the game.

Alter Crafting [Retired] 1.9.5
A new crafting system for Minecraft servers!