{
  "version": 3,
  "created_at": "2026-07-08T15:55:13.693Z",
  "task_summary": "Update Paper D (agentic-workflow manuscript) with three new correction episodes + refreshed metrics/citations",
  "agents": [],
  "phases": [
    {
      "name": "Plan",
      "delegations": [
        {
          "steps": [
            {
              "title": "Audit 12h of new artifacts + confirm episodes",
              "description": "Systematically review all artifacts created since the last Paper D save (index-case suite, Hill 2025.pdf, recruitment doc v1-v5, exhaustive literature review, atopic-march, dx-assay design). Confirm and precisely characterize each correction episode against its source artifact: (6) recruitment-ethics HLA-stratification→HLA-agnostic; (7) Hill 2025 TCR paper trajectory shift + β-casein panel gap; (8) index-case 'presentation≠pathology' wheat false-positive assumption. Scan for any additional episodes (e.g. allele-frequency table caveat, DQ2.2 approximation). Produce handoff/new_episodes.json with episode/claim/trigger/caught_by/resolution/impact/type for each."
            },
            {
              "title": "Recompute campaign metrics (Table 1)",
              "description": "Run compute_campaign_metrics on the current artifact store (now grown well beyond 147) and compute_active_span_hours from artifact timestamps. Rebuild table1_campaign_metrics.csv + .png with sub-rows reconciling to the new headline (add 'other' row if needed). Version the same T1 artifacts. Verify measured-vs-framed: active-compute span from timestamps, not the calendar window."
            },
            {
              "title": "Append episodes to correction ledger (Table 2)",
              "description": "Append the 3 (or more) confirmed episodes to correction_ledger_T2.csv with terse, factual wording, each traceable to its source artifact. Keep the episode-type taxonomy (Human domain catch / Agent self-correction / Contradiction contained / Uncertainty calibrated / Novel claim validated). Recalculate the calibration partition (grounded = confirmatory + confirmatory-with-novel-emphasis; contradictory NOT grounded). Version the same T2 artifact."
            },
            {
              "title": "Re-render Figure 3 (correction ledger)",
              "description": "Pull Fig 3 build code from its artifact lineage, extend the per-episode accent-color list, add the new episode rows, update Panel a calibration counts. Verify 0 real text overlaps and correct arithmetic in the caption. Save as a new version of figure3_correction_ledger.png. Publication-grade via figure-style."
            },
            {
              "title": "Update manuscript prose",
              "description": "Update paperD_nature_perspective.md: expand the 'Calibration and self-correction' section with the three new episodes (esp. the index-case 'presentation≠pathology' lesson and the recruitment-ethics catch as exemplars of human supervision); add a short passage on how the Hill 2025 paper redirected the pMHC work toward functional TCR ground truth; refresh 'What the campaign found' if the pMHC/index-case work is now in scope; update metric strings to match recomputed Table 1. Keep Nature Perspective register."
            },
            {
              "title": "Verify citations + re-render DOCX",
              "description": "Verify all DOIs (including Hill 2025 doi:10.1016/j.jaci.2025.01.008 and any new refs) against CrossRef before they enter text. Resolve figure markers to paths, render paperD_nature_perspective.docx, verify embedded image count + key strings via zipfile. Version both md and docx artifacts."
            },
            {
              "title": "Update skill manifest",
              "description": "Update the agentic-campaign-manuscript skill: move the queued recruitment-ethics episode into 'Recorded episodes', add the Hill/index-case episodes, refresh the deliverable-manifest artifact IDs to the new versions, and republish via host.skills.edit + host.skills.publish."
            }
          ]
        }
      ],
      "id": "phase-0"
    }
  ],
  "desired_outputs": [
    "Updated correction ledger (Table 2) with new episodes appended",
    "Updated Figure 3 (correction ledger) reflecting new episode count + recalculated calibration",
    "Refreshed Table 1 campaign metrics (recomputed from current artifact store)",
    "Updated Paper D manuscript prose (md) incorporating the three episodes + Hill trajectory shift",
    "Re-rendered Paper D DOCX with verified citations",
    "Updated agentic-campaign-manuscript skill manifest"
  ],
  "feasibility": {
    "rationale": "All three flagged episodes are documented in artifacts created in the last 12 h (index_case_groundtruth_calibration.md, Hill 2025.pdf, recruitment_stratification_rationale.md v1→v5), so each ledger entry is traceable to source rather than reconstructed. The manuscript, figures, and skill all have continuous lineage to version cleanly.",
    "confidence": "high"
  }
}