v0.3.1 — reference accuracy fixes

Accuracy fixes in the reference material, each checked against the upstream
sources (Doctrine ORM 3.7, Symfony 7.4 and 8.1, API Platform 4).

Fixed

• Doctrine: ORM 3 did not remove setFetchMode(), and PARTIAL is back
  from ORM 3.3; the fetch-modes skill, its description and three agents said
  otherwise. clear() takes no argument in ORM 3, and proxy initialization is
  checked with isUninitializedObject().
• API Platform: #[RateLimit] does nothing on an #[ApiResource] (it is
  read from the controller), so the security example now limits in a state
  processor. Test examples use the v4 defaults (member, totalItems, 30
  items per page). The versioning listener sends an RFC 9745 Deprecation
  value, and its tests no longer use an undefined client.
• Messenger: the retry strategy relied on a SentStamp::getSentAt() that
  does not exist; the failed-message service is typed
  ListableReceiverInterface. Scheduler examples pass from, until and the
  timezone as arguments, and no longer call PostRunEvent::getDuration().
• Tests: #[DataProvider] instead of the annotation, mocks of the
  EntityManager scoped to orchestration tests, and the Prophecy dependency
  stated.