3000 lines of spaghetti code is one thing. But this code is pretty-well modularized. The author obviously knows what he's doing.

Maybe he finds it easier to jump around the file that way. I know I've built up projects like that. When it starts to transition from tech demo to real product, I would probably break it up into different files (util.js, lexer.js, etc). But no harm in the meantime.

A simple web app spread across 42 files might actually be terrible and over-engineered. Or it might not. The moral is: don't judge code quality by isolated metrics.