Fix container_repositories index repair to handle 1-to-1 relationship

What does this MR do and why?

This backports !217242 (merged) to 18-6-stable-ee.

The container_repository_states table has a primary key constraint on container_repository_id, enforcing a one-to-one relationship with container_repositories. When duplicate container_repositories entries exist, previously the repair task attempted to update all container_repository_states references to point to the "good" ID, which violated the primary key constraint when a state entry already existed for that ID.

For example, suppose the container_repositories table:

id	project_id	name
1	1000	test
2	1000	test
3	1000	test

With this container_repository_states table:

container_repository_id	verified_at
1	2025-12-01
2	2025-12-02
3	2025-12-03

The old approach tried to fix the duplication in container_repository_states by remapping the container_repository_id:

  UPDATE container_repository_states SET container_repository_id = 3
  WHERE container_repository_id IN (1)

However, this failed with:

  PG::UniqueViolation: duplicate key value violates unique constraint
  "container_repository_states_pkey"

The fix adds a new delete_orphaned option to reference configurations. When set to true, the repair task deletes all references pointing to the duplicate (bad) IDs before deleting the duplicate records. This approach:

1. Deletes the container_repository_states rows for duplicate IDs.
2. Deletes the duplicate container_repository rows.
3. Preserves the state entry for the good ID.

This is simpler and more appropriate than using deduplication_column for one-to-one relationships where we don't need to preserve the orphaned references.

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