The compiler can't really change things like the class hierarchy, and a lot of the more interesting optimizations are done at runtime.

Right. If you're coming from a C background, you'd be amazed how much information from the source is preserved in a Java .class file. To my knowledge, C++ turns into a binary blob, and a lot of magic can happen along the way. But Java turns into a slightly more machine-readable version of Java. A lot of the structure in the code is actually directly meaningful to the JVM. All the details of the object -- its variable names and types, its methods and their signatures, the class hierarchy, even sometimes the line number in the original source code -- is still there. The preservation is so complete that it has been said all Java programs are essentially open source (the sort of thing people would normally say about, say, Javascript).

Now, last time I played with Minecraft, it had been run through an obfuscator as well, so some of that doesn't apply. In particular, the variable and method names have been reduced to gibberish, and I don't know what sort of monkey business might have occured around inlining constants.

But macro structure doesn't change. In Java, given the way .class files work, it really can't change. And that's where a lot of the abstraction in a project lives. The class hierarchy is still there. Use of interfaces is still there. How you organize data, how you manufacture objects, which function calls which function, it's all still there. Even little things, like whether your functions return objects, enumerations, or magic numbers, is unchanged.

Even in decompiled code, even right at the start, you can blur your eyes, and at a glance you'll see either a lot of little functions or a few big ones, a lot of little classes or a few big ones, a lot of inheritance relationships through abstract classes or a few simple ones.