I need some help. I would like to be able to use the /water and /lava command on my server. I really only need to know one thing. When the World of Minecraft servers were created was the Minecraft_Server.jar file edited to allow those commands, or was an entire new file created to run them?

Please help, I know java enough to understand .jar, .class, .mf, and all those files, so please give me a full explanation. 

Thanks,

-Rayboy