Comment by Shared404

Except instead of config files, Windows has the registry.

Also, as mentioned by the siblings to thia comment, the 'mess' has a purpose, and is less messy than it appears.

Want to manually install something? Into /usr/local it goes. Done.

The only way to handle this that I've been really impressed with is Mac's "Applications" folder. Unfortunately, I dislike most other things about Mac.