Auto-refine loop for structure planner to reach coverage/dependency requirements

[zhongkaifu]

Motivation

• The structure planner returned a skeleton even when finalize_workflow indicated more work was needed, causing misleading WARN messages and stopping further refinement.
• The goal is to automatically continue planning rounds until coverage passes, there are no nodes without upstream, and ready=True, within configured retry limits.

Description

• Track finalize feedback and nodes missing upstream by adding latest_finalize_feedback and latest_nodes_without_upstream and expose them from finalize_workflow.
• Introduce _run_agent helper and an auto-refine while loop that reruns the Agent with feedback, bounded by max_coverage_refine_rounds and max_dependency_refine_rounds.
• Update the planner to append system feedback to run_input, increment refinement counters, and log auto-refine rounds via log_info.
• Clarify warning messages when finalize_workflow was never called versus when coverage/dependency checks failed and prepare the skeleton only after refinement stops.

Testing

• No automated tests were executed for this change.
• Static searches (rg/sed) were used during development to locate related logic and verify edits, but these are not automated tests.

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Codex Task