Thanks for the replies. I am very, very new to this, but I am an experienced Java developer so should not be too hard.
What is ASM?
Other than directly modding the source, how can I get to the list to modify it?
Ok, I am looking to change some default functionality (recipes and crafting) and replace it with my own stuff. Does MCF allow this and/or anyone know how to do it without changing the core minecraft/minecraft_server.jar?