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PR #9872 — fix(cli): preserve legacy root prefill_messages_file support

Summary of Changes

This PR adds backward compatibility for the root-level prefill_messages_file config key by copying it into the agent.prefill_messages_file section when the nested key is absent. This matches the pattern already used for other legacy root-level keys like model and max_turns.

Review

Correctness ✅

• The precedence logic is correct: an explicit agent.prefill_messages_file takes priority over the legacy root key. This matches the established pattern in the same function.
• The guard condition properly checks isinstance(agent_file_config, dict) before calling .get(), avoiding potential AttributeError on non-dict values.

Testing ✅

• Two well-structured test cases cover the happy path (root key copied) and the precedence path (nested key wins). These are the exact scenarios that matter.

Readability ✅

• The inline comment clearly explains the intent and rationale.
• The code is minimal and follows the existing pattern in the same block (see the max_turns handling above).

Summary

Clean backward-compatibility fix that follows the established pattern in load_cli_config. Tests cover both code paths.

Assessment: approve

Superseded by #38760, which merged the broader fix: top-level prefill_messages_file is now canonical across cli/gateway/cron with agent.prefill_messages_file retained as a legacy fallback. Closing as completed since the underlying issue (#9635) is now fixed on main.