Disease Market Sizing Orchestration

Phase Sequence

1. contract-elicitor → .cache/<slug>/contract.json
2. disease-stratifier → .cache/<slug>/staging.json
3. Evidence Recall (inline 7 retrieval + A1' guidelines) → .cache/<slug>/sources/
4. Compose-then-Audit double-turn (≤ 3 turns) → output/<slug>/report_raw.html draft + verification_report.json
5. Bundle + Design + TOC → output/<slug>/report_standalone.html + report_data.xlsx + delivery_manifest.json (PDF only when explicitly requested)

Production Non-Negotiables

• Production smoke must start from plugin-session bootstrap evidence: .cache/<slug>/agent_run_context.json with mode=agent-plugin-bootstrap, agent_runtime=codex_or_claude_code_plugin_session, and requires_user_api_key=false.
• Production smoke must continue through the reusable plugin continuation entrypoint and write .cache/<slug>/plugin_session_invocation.json; direct temporary callback scripts are not valid production-pass evidence.
• Disease-specific callbacks may adapt inputs or act as deterministic test doubles, but a production pass is invalid if a callback directly writes the final report or market model in place of reusable skills.
• Do not use one-off scripts/generate_*smoke_report.py generators or handwritten skill_run_log.json entries as production evidence.
• Every production run must write deliverables under a dedicated output/<slug>/ directory; do not overwrite root-level or previous-run report files.
• The orchestrator must write .cache/<slug>/orchestration_trace.json with entrypoint=disease-market-sizing-orchestration, agent_runtime=codex_or_claude_code_plugin_session, a non-empty run_id, status=ok, and ok phases for disease-stratifier, evidence-recall, cite-bound-content-generator, content-verification-layer, mermaid-renderer, and report-bundle-builder.
• Downstream skill_run_log.json entries must be emitted by the same orchestrator run with generated_by=disease-market-sizing-orchestration and matching run_id; logs without this trace are invalid for production smoke.
• Evidence recall must use multiple retrieval channels and must not stop at the >50 literature hard floor when the disease area is source-rich; respiratory IFI-like topics should normally exceed 100 saved literature sources.
• Retrieval channel entries must carry provenance. pubmed-search, europepmc-search, clinical-trials-search, bioc-fulltext-fetch, pubtator-entity-search, medical-evidence-grading, and market recall entries in skill_run_log.json need generated_by / run_id plus a link to the orchestration run that consumed them.
• Fetched required channels must enter the body analysis. If ClinicalTrials.gov/AACT or PubTator/entity sources are saved under .cache/<slug>/sources/, production verification must require matching [nct:...] / [aact:...] / [pubtator:...] anchors or a recorded pre-verification exclusion reason.
• Evidence grading must affect source utilization. D-grade PubMed records may stay in background/reference appendices, but production smoke must block D-grade PMIDs used as analytical body anchors. Grading may use publication types and conservative study-design terms found in the saved PubMed title/abstract, but must not use external disease/drug dictionaries.
• Production compose must call cite-bound-content-generator.compose(..., return_report=True) and pass ComposedReport.sub_pages / toc_anchors to report-bundle-builder.
• Production compose must be agent-authored or reusable-skill-authored. The preferred plugin contract is .cache/<slug>/agent_authored_compose.json read by an adapter-only callback. compose_authoring_provenance.json must prove authoring_mode=agent_authored_compose_artifact and generated_by=codex_or_claude_code_plugin_executor; callback-authored HTML/formula/Mermaid is invalid.
• The agent-authored compose artifact must be a formal plugin phase, not an unexplained prewritten JSON. Pair it with .cache/<slug>/agent_authored_compose_manifest.json containing prompt digest, source tree digest, artifact checksum, current source slug, and validation time; production smoke must block missing or checksum-mismatched manifests.
• Production continuation accepts only final agent-authored compose artifacts: provenance.phase=final, current source_run_slug, reader_layer.html, audit_layer.evidence_support_table, audit_layer.reader_to_audit_mapping, substantive claims, current-run source_usage, formula_dag_ref, and mermaid_sources. Precompose artifacts are checkpoint evidence only and must block before smoke.
• Production verification must fail closed with semantic verification, source manifest provenance when available, and persisted anchor_audit metrics in verification_report.json.
• When semantic verification writes .cache/<slug>/semantic_audit_log.jsonl, verification_report.json must link that log and record matching non-empty entry counts. Otherwise the audit is not explainable and production smoke must fail.
• Production verification must block formula/model evidence citation dominance and evidence-digest-matrix body dominance. These are signs that the pipeline emitted a calculation dump or source-processing log instead of a V25-level report.
• Drug citation verification must scan the reader HTML plus audit-layer claims together. Audit claims alone are not enough because a reader-layer report can contain drug names that the audit layer omits; production smoke blocks zero drug mentions when antifungal drug names are visible.
• Production verification must require core evidence synthesis in the body when recall is broad. A V25-level report needs thematic literature digestion across cohorts/pathways/LP decisions plus growth drivers, payer/access impact, LP ranking methodology, and methods/sensitivity depth.
• Mermaid rendering must write .cache/<slug>/mermaid_render_manifest.json; decision-tree PNGs without this manifest are invalid. The extractor must match any <div> whose class list contains mermaid, including tags with attributes such as data-chart; HTML attributes cannot cause the renderer to skip flowchart blocks.
• Each Mermaid manifest block must self-describe graph quality with edge_count, decision_node_count, numeric_evidence_count, and cross_point_count. A manifest that only says render ok/path/source is insufficient for V25-level auditability.
• A compose artifact that fails verification is a failed draft only. It must not be treated as a latest deliverable candidate until verification_report.verdict=ok, rendered Mermaid assets exist, and bundle/smoke gates pass.
• Before production smoke audit, standalone HTML should embed the current source/citation/verification corpus as an audit package when the project provides scripts/embed_source_corpus.py; size parity must come from useful provenance, not fake padding images.
• Production smoke audit is mandatory before reporting a pass against V25. Count/size/image metrics are insufficient without sub-page depth, meaningful body source utilization, numeric evidence support, and Mermaid cross-point source checks.

Functions

• run(user_one_liner, project_root, callbacks, *, report_output_dir=None, v25_reference_html=None, require_production_smoke_audit=None) -> manifest dict