I should add: When you have a ton of code in a single file, Code Climate will start to assess penalties. The idea is to try to approximate how maintainable and approachable a given piece of code would feel to a developer who is looking at it. It's not perfect, but very large files tend to be harder to maintain in general.

So Underscore's choice to be single file effectively dooms it from the start. Ember.js, on the other hand, is larger but more decomposed and scores fairly well.