Every single codebase doing anything nontrivial is mess. Show me a code base that you can marvel at it's beauty, elegance, and how neat and tidy everything is organized and one of two things will be true about it.

1. It has never touched the real world, real hardware, or real users.

2. All the mess is hidden in some dependencies that handle the integration points with the outside world.

You cannot escape the fact that the world is full of sharp edge cases, no perfect abstraction exists, all models of the real world are approximate, there is no architecture that survives changes to business requirements, and all assumptions made about the environment where your code runs will eventually be false, which makes a mess out of code that was once nice and tidy.