by-name: make the way of adding packages clearer

The structure of this directory maps almost directly to top-level package attributes.

This is the recommended way to add new top-level packages to Nixpkgs [when possible](#limitations).

Packages found in the named-based structure do not need to be explicitly added to the

`top-level/all-packages.nix` file unless they require overriding the default value

of an implicit attribute (see below).

## Example

The top-level package `pkgs.some-package` may be declared by setting up this file structure: