rootcause-mcp: Skill for Claude Code

RootCause Clinical Reasoning Harness

Use RootCause MCP as an auditable reasoning ledger, not as an autonomous clinician. Keep observations, interpretations, hypotheses, and causal claims visibly separate.

Load the case contract

Read references/case-handoff.md before starting, resuming, handing off, or finalizing a case. Before writing case state, also read clinical://contracts/case-input-manifest and clinical://contracts/case-analysis-report; treat those live JSON Schemas as authoritative over copied examples.

Read references/clinician-ddx-discussion-zh-tw.md when expanding a differential or preparing clinician-facing Traditional Chinese output. It defines the bounded breadth, candidate-level reasoning, language, and quantification rules; do not load it for a code-only repository task.

Select the tool surface

• Discover the advertised tools before acting; never call an unadvertised tool or facade action.
• Prefer condensed for the 8-tool workflow facade or all for the complete 46-tool surface. Consult the mapping for discrete-only operations.
• Treat clinical and rca as partial profiles. Hand off the same session_id and ledger to an agent/profile with the missing tools rather than silently skipping stages.
• Reuse the handed-off session_id. Never create a second case because an intermediate tool returns no state.

Follow every stage in order

1. Case/session — Start or resume one de-identified case. Record scope, analysis purpose, timezone, profile, and stable session ID.
2. Multi-source manifest — Pass a schema-version 1.0 source_manifest to session creation. Register every supplied document with a stable ID, approved URI, whole-file SHA-256, media type, source kind, and extraction state before extracting findings.
3. Source review — After extraction, append an authorized rc_adjudicate_source event for every registered source. Record processing status, de-identification, independence/group lineage, reviewer, and rationale without changing the pinned manifest identity or digest.
4. Exact evidence and time — Add one atomic finding per evidence item with document ID, exact snippet, precise location, and a typed source-faithful temporal record. Only use kind=instant when the source includes an explicit offset; retain date, range, relative, or unknown without inventing order. Verify exact text when possible; retain UNVERIFIED otherwise.
5. Differential expansion — Build the maximum reasonable mechanism-based DDx for the phenotype and time course. Choose a syndrome-appropriate framework and persist a PRIMARY breadth audit after reviewing every required framework cell; a final audit may retain REVIEWED_INSUFFICIENT_DATA with unknowns and typed discriminators but no NOT_ASSESSED. Three unique diagnoses, two non-UNKNOWN mechanisms, and one applicable must-not-miss diagnosis are deterministic finalization floors, not a clinical target or cap. Prune duplicate labels and candidates with no plausible mechanism or decision impact instead of producing an unbounded laundry list.
6. Candidate disposition — For every active diagnosis, persist why it was considered, mechanism_category, diagnostic_role, reasoning_basis, qualitative certainty, source-linked support/refutation/neutral evidence, candidate-specific unknowns, and either genuine evidence or a typed discriminating test. A must-not-miss flag expresses safety priority, not likelihood. Use rc_select_leading_hypothesis with a reason and actor; never let numeric compatibility or array order choose the lead.
7. Evidence testing — Link evidence using the direct applied LR. Use LR > 1 for support, LR < 1 for contradiction, and 1.0 when neutral or quantitatively unknown; neutral links do not count as support or refutation. A non-neutral LR requires both the target patient evidence and a distinct verified LITERATURE evidence record that preserves the quantitative source. Never invent or invert an LR or present an uncalibrated compatibility prior/posterior as clinical probability. When refuting evidence is pending, persist a typed planned_tests entry with purpose, expected supporting/refuting results, and PLANNED or ORDERED status.
8. Uncertainty and bias — Treat unknowns as inputs: say which mechanisms remain open and what result would discriminate them. Keep source observation, host/clinical inference, and causal claim explicitly separate. Record concise rationale, missing data, competing explanations, disconfirming tests, and anchoring/confirmation/premature-closure risks. Do not emit hidden chain-of-thought or private scratch work.
9. System RCA — Build Fishbone and Why structures. Persist an authorized HFACS review for every Fishbone cause as CONFIRMED with a recognized code or NOT_APPLICABLE without a code; suggestions and codes supplied while adding a cause remain unreviewed. Persist a causation-review attempt linked to every proposed root. Keep the Why/root/audit ID, exact description, and evidence ID set identical. The validator is a conservative proof-obligation audit, not clinical causal proof: omit REJECTED claims from the root-cause bucket, retain INSUFFICIENT_DATA only as PROPOSED, and label an audit pass AUDIT_OBLIGATIONS_PASSED even if a compatibility enum says VERIFIED.
10. Readiness and review — Run conflict/readiness checks. Keep the case preliminary until named qualified humans review sources, HFACS dispositions, clinical safety, causal claims, and proposed actions. Manual evidence confirmation, source/HFACS adjudication, and finalization are valid only when the named reviewer is present in the operator-controlled ROOTCAUSE_AUTHORIZED_REVIEWERS allowlist; allowlist membership alone does not establish clinical qualification.
11. Unified output — Produce the standardized handoff/report package in the reference. For the built-in clinician renderer, request Markdown with locale="zh-TW" and audience="clinician"; JSON/FHIR payload values and custom templates retain their original language. Preview before finalization, inspect machine-readable conformance_checks[], and identify every incomplete or unverified section. Finalization must recompute every hard check using the operator-supplied reviewer allowlist and include reviewer, timezone-aware time, and a recomputable content hash. The domain snapshot rejects nested mutation; the hash is integrity metadata, not durable WORM storage.