Correct Attractor spec inconsistencies

[btomaj]

• Transform.apply(graph) was inconsistently also defined as Transform.transform(graph).
• Orphan nodes were inconsistently expected to result in both error and warning.
• run(...) in core execution loop accepted both a context and a config as the second parameter.
• Outcome.status was inconsistently both an enum and a string.
• Edge shape was implied to contain both target and to_node for the same purpose.
• Context behaviour was unspecified for loop_restart=true
• StageStatus==FAIL was inconsistently expected to both terminate and retry.
• wait.human was inconsistently expected to return preferred_label in its Outcome

[jaytaylor]

@btomaj Rather than listing what was changed, it will be more informative if you can share what effect these changes have in terms of generated functionality.

Have you performed generation activities with the main branch as well as this PR branch? What was the difference in outcome?

[btomaj]

@jaytaylor I picked up each of these inconsistencies when Codex failed to converge. Repeated runs identified implementation gaps ad nauseam, which revealed conflicts or underspecifications in the spec. I didn't know the correct solution, so I guessed.