> Java basically does the same thing and I've never heard anyone complaining about that.

I don't love dealing with Java, but it has none of these particular issues. It's easy to find the definition of a class, because it enforces that the file path must match the fully qualified class name for all public classes (and this tends to be followed for privates as well in practice). Finding the implementation isn't quite trivial, but if you know a class in the tree then you can easily find the whole parent tree by following the "extends Foo" clauses, or find subclasses by grepping for it instead.