Greptile Summary

This PR extracts the final "confirm/write" step of the doctor config flow into a dedicated finalizeDoctorConfigFlow helper, reducing the surface area of loadAndMaybeMigrateDoctorConfig and making the three decision branches (preview-accept, preview-decline, repair-auto) independently testable.

• Correctness: The refactoring faithfully preserves the original logic. Returning params.cfg (not params.candidate) in repair mode is intentional — by the time finalizeDoctorConfigFlow is called, runDoctorRepairSequence has already updated cfg in place.
• Test coverage: The two preview-path tests (confirm and decline) are thorough and use distinct cfg/candidate objects. The repair-mode test covers the right scenario but passes identical values for cfg and candidate, so it cannot detect a regression where the wrong object is returned (see inline comment).
• No behavioral change: The shouldWriteConfig local removed from the caller was the only other change; all callsites receive equivalent behavior through finalized.shouldWriteConfig.

Confidence Score: 5/5

• This PR is safe to merge — it is a pure refactoring with no behavioral changes and adds targeted test coverage.
• The extracted logic is a verbatim translation of the original inline code with no semantic differences. The only note is a minor test-coverage gap in the repair-mode test (identical cfg/candidate values), which is a non-blocking follow-up and does not affect correctness.
• No files require special attention; the minor test improvement is tracked in the inline comment on finalize-config-flow.test.ts.

This is a comment left during a code review.
Path: src/commands/doctor/finalize-config-flow.test.ts
Line: 46-61

Comment:
**Repair-mode test doesn't distinguish `cfg` from `candidate`**

In this test `cfg` and `candidate` are set to identical values, so the assertion passes regardless of whether the implementation returns `params.cfg` or `params.candidate`. In repair mode the intent is to return the already-repaired `cfg` (updated upstream by `runDoctorRepairSequence`), but a future refactor that accidentally returned `params.candidate` here would go undetected.

Consider using distinct objects so the test pins the exact returned value:

```suggestion
  it("writes automatically in repair mode when changes exist", async () => {
    const result = await finalizeDoctorConfigFlow({
      cfg: { channels: { signal: { enabled: true } } },
      candidate: { channels: { signal: { enabled: false } } }, // deliberately different
      pendingChanges: true,
      shouldRepair: true,
      fixHints: [],
      confirm: async () => true,
      note: vi.fn(),
    });

    expect(result).toEqual({
      cfg: { channels: { signal: { enabled: true } } }, // cfg, not candidate
      shouldWriteConfig: true,
    });
  });
```

How can I resolve this? If you propose a fix, please make it concise.

_{Last reviewed commit: "refactor(doctor): ex..."}