Not changing semantics, but changed the wording to make it clearer.

- Provided an object hierarchy of objects in a Mu IR bundle. This
  describes the "has many" and "refers to" relations between things in a
  bundle.

- Clarify what are "top-level entities". Specifically, "functions" are,
  but "function versions" are not. Stopped using "top-level definitions"
  because "definition" is too text-oriented. The API functions create
  entities.

- Stopped using the term "declaring a function", but use "creating a
  function" and "creating a function version" instead. Now "undefined
  function" and "defined function" simply refers to functions with 0
  versions and functions with 1+ versions, respectively.

- Explicitly state the "function version lookup" when a function is
  executed.