It's not written to be "modified". It's not written with a specific modular outcome in mind. It's more often than not a one-off messy code that gets the job done, because that's the requirements and the pace of the industry.
And, especially for something like Minecraft, it has to be original and even explore the problem space and ideas in the process of building it. It's not something you do based on a design carved in stone, with some cushy strict waterfall method or what have you.
Building games, and especially such games, is an explorative process, and one-off process, and a war on many fronts (e.g with time, or with tons of competing gameplay ideas).
You are only able to say what you say, because you look at the code in hindsight.