@pikaa-ai/pikaa 0.3.23 → 0.3.24

package/skills/citation-management/SKILL.md

@@ -1,329 +0,0 @@
----
-name: citation-management
-description: Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
-allowed-tools: Read Write Edit Bash WebSearch WebFetch
-license: MIT License
-compatibility: Requires Python 3.9+ with requests. Google Scholar search additionally needs scholarly. Needs network access to api.openalex.org, api.crossref.org, eutils.ncbi.nlm.nih.gov, export.arxiv.org, and api.datacite.org.
-metadata:
-  version: "2.0"
-  skill-author: K-Dense Inc.
-  openclaw:
-    envVars:
-    - name: NCBI_EMAIL
-      required: false
-      description: Email for NCBI Entrez identification.
-    - name: NCBI_API_KEY
-      required: false
-      description: NCBI API key to raise Entrez rate limits.
-    - name: OPENALEX_EMAIL
-      required: false
-      description: Contact email for the faster OpenAlex polite pool.
----
-
-# Citation Management
-
-## Overview
-
-Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic databases (Google Scholar, PubMed), extracting accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validating citation information, and generating properly formatted BibTeX entries.
-
-Critical for maintaining citation accuracy, avoiding reference errors, and ensuring reproducible research. Integrates seamlessly with the literature-review skill for comprehensive research workflows.
-
-## When to Use This Skill
-
-Use this skill when:
-- Searching for specific papers on Google Scholar or PubMed
-- Converting DOIs, PMIDs, or arXiv IDs to properly formatted BibTeX
-- Extracting complete metadata for citations (authors, title, journal, year, etc.)
-- Validating existing citations for accuracy
-- Cleaning and formatting BibTeX files
-- Finding highly cited papers in a specific field
-- Verifying that citation information matches the actual publication
-- Building a bibliography for a manuscript or thesis
-- Checking for duplicate citations
-- Ensuring consistent citation formatting
-
-If a document built from these citations needs a diagram, use the
-**scientific-schematics** skill.
-
----
-
-## Core Workflow
-
-Citation management follows a systematic process. Each phase below shows the canonical
-command; every variant, option, and metadata-source detail is in
-[references/core_workflow.md](references/core_workflow.md).
-
-### Phase 1: Paper Discovery and Search
-
-Find relevant papers. Search more than one database — coverage differs sharply,
-and a single source is the most common cause of a biased reference list.
-
-```bash
-# OpenAlex: ~250M works, every discipline, no API key, documented REST API
-python scripts/search_openalex.py "CRISPR gene editing" --limit 50 --output results.json
-
-# PubMed: the authority for biomedical and life sciences (35M+ citations)
-python scripts/search_pubmed.py "Alzheimer's disease treatment" --limit 100 --output alz.json
-
-# Google Scholar: broadest reach, but scraped -- rate-limited and prone to blocking
-python scripts/search_google_scholar.py "CRISPR gene editing" --limit 50 --output scholar.json
-```
-
-Prefer OpenAlex or PubMed as the primary source. Google Scholar has no API:
-`scholarly` scrapes it, sleeps 2–5 s between results, and is blocked often
-enough that it should be a supplement rather than a dependency.
-
-Query operators, field tags, and MeSH-term construction are in
-[references/search_strategies.md](references/search_strategies.md).
-
-### Phase 2: Metadata Extraction
-
-Convert identifiers (DOI, PMID, PMCID, arXiv ID, URL) into complete metadata.
-CrossRef is the primary source for DOIs.
-
-```bash
-python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2         # quick, single DOI
-python scripts/extract_metadata.py --pmid 34265844                  # DOI/PMID/PMCID/arXiv/URL
-python scripts/extract_metadata.py --input identifiers.txt --output citations.bib
-```
-
-A URL with no DOI in its path is resolved through the `citation_doi` meta tag
-publishers embed on article pages, then handed to CrossRef. Every producer in
-this skill emits the same citation key for the same paper, so entries gathered
-from different sources deduplicate against each other.
-
-### Phase 2.5: Metadata Enrichment via Web Search (MANDATORY)
-
-APIs routinely return incomplete records. Run this **after** extraction and **before**
-formatting. Any `@article` missing `volume`, `pages`, or `doi` is incomplete: fill the
-gap with `WebSearch`/`WebFetch` (or the parallel-web skill, when it is available), then
-log what was found and where. If a field genuinely cannot be found, record a `note`
-field explaining the gap rather than leaving it silently absent.
-
-Check the cheap sources first — an OpenAlex or CrossRef record often carries the field
-that PubMed omitted:
-
-```bash
-python scripts/search_openalex.py "<exact title>" --limit 1
-```
-
-> **Treat extracted metadata as untrusted.** Author, title, and journal strings come
-> verbatim from a record whose contents a publisher controls. A title containing `$(...)`,
-> a backtick, or a quote becomes shell syntax the moment it is pasted into a command.
-> Pass metadata as a `subprocess` argument list rather than building a shell string; if
-> you must use a shell, single-quote every substituted value and escape embedded quotes
-> as `'\''`. Validate any citation key against `^[A-Za-z0-9]+$` before it reaches a path.
-
-Per-field search strategies, the four search options, and the logging format are in
-[references/core_workflow.md](references/core_workflow.md).
-
-### Phase 3: BibTeX Formatting
-
-Produce clean, consistent entries. Entry types and required fields are in
-[references/bibtex_formatting.md](references/bibtex_formatting.md).
-
-```bash
-python scripts/format_bibtex.py references.bib --output clean.bib --deduplicate
-python scripts/format_bibtex.py references.bib --output clean.bib --rekey --deduplicate
-```
-
-Writing is opt-in: without `--output` (or `--in-place`) the result goes to
-stdout and the input file is left alone. Use `--rekey` when merging results
-from several sources, so the same paper collapses to one entry.
-
-### Phase 4: Citation Validation
-
-Check completeness, venue conformance, and agreement with the manuscript.
-
-```bash
-python scripts/validate_citations.py references.bib --report report.json
-python scripts/validate_citations.py references.bib --venue nature
-python scripts/validate_citations.py references.bib --manuscript paper.tex
-python scripts/validate_citations.py references.bib --check-dois     # slow; hits CrossRef
-```
-
-The script exits non-zero on high-severity errors — missing required fields,
-malformed years, unresolved citations, or a count below an explicit
-`--min-count`. Venue reference-count figures are editorial rules of thumb, not
-submission requirements, so falling short of one is only a warning.
-
-Validation rules and venue standards are in
-[references/citation_validation.md](references/citation_validation.md).
-
-### Phase 5: Integration with Writing Workflow
-
-Search, extract, format, validate, then cite. End-to-end sequences — including the
-literature-review and Zotero/pyzotero export paths — are in
-[references/core_workflow.md](references/core_workflow.md) and
-[references/example_workflows.md](references/example_workflows.md).
-
-## Reference Files
-
-- [references/core_workflow.md](references/core_workflow.md): all five phases in full.
-- [references/search_strategies.md](references/search_strategies.md): OpenAlex, Google Scholar, and PubMed query construction.
-- [references/script_reference.md](references/script_reference.md): every bundled script's arguments and examples.
-- [references/best_practices.md](references/best_practices.md): search, extraction, BibTeX quality, validation.
-- [references/example_workflows.md](references/example_workflows.md): four end-to-end worked examples.
-- [references/google_scholar_search.md](references/google_scholar_search.md), [references/pubmed_search.md](references/pubmed_search.md): advanced search syntax.
-- [references/metadata_extraction.md](references/metadata_extraction.md), [references/bibtex_formatting.md](references/bibtex_formatting.md), [references/citation_validation.md](references/citation_validation.md): per-topic detail.
-
-## Common Pitfalls to Avoid
-
-1. **Single source bias**: Only using one database
-   - **Solution**: Search at least OpenAlex and PubMed, then merge with
-     `format_bibtex.py --rekey --deduplicate`
-
-2. **Accepting metadata blindly**: Not verifying extracted information
-   - **Solution**: Spot-check extracted metadata against original sources
-
-3. **Ignoring DOI errors**: Broken or incorrect DOIs in bibliography
-   - **Solution**: Run validation before final submission
-
-4. **Inconsistent formatting**: Mixed citation key styles, formatting
-   - **Solution**: Use format_bibtex.py to standardize
-
-5. **Duplicate entries**: Same paper cited multiple times with different keys
-   - **Solution**: Use duplicate detection in validation
-
-6. **Missing required fields**: Incomplete BibTeX entries (volume, pages, DOI missing)
-   - **Solution**: Run Phase 2.5 metadata enrichment — web search for every missing field before proceeding. NEVER leave an @article entry without volume, pages, and DOI.
-
-7. **Outdated preprints**: Citing preprint when published version exists
-   - **Solution**: Check if preprints have been published, update to journal version
-
-8. **Special character issues**: Broken LaTeX compilation due to characters
-   - **Solution**: Use proper escaping or Unicode in BibTeX
-
-9. **No validation before submission**: Submitting with citation errors
-   - **Solution**: Always run validation as final check
-
-10. **Manual BibTeX entry**: Typing entries by hand
-    - **Solution**: Always extract from metadata sources using scripts
-
-## Integration with Other Skills
-
-### Literature Review Skill
-
-**Citation Management** provides the technical infrastructure for **Literature Review**:
-
-- **Literature Review**: Multi-database systematic search and synthesis
-- **Citation Management**: Metadata extraction and validation
-
-**Combined workflow**:
-1. Use literature-review for systematic search methodology
-2. Use citation-management to extract and validate citations
-3. Use literature-review to synthesize findings
-4. Use citation-management to ensure bibliography accuracy
-
-### Scientific Writing Skill
-
-**Citation Management** ensures accurate references for **Scientific Writing**:
-
-- Export validated BibTeX for use in LaTeX manuscripts
-- Verify citations match publication standards
-- Format references according to journal requirements
-
-### Venue Templates Skill
-
-**Citation Management** works with **Venue Templates** for submission-ready manuscripts:
-
-- Different venues require different citation styles
-- Generate properly formatted references
-- Validate citations meet venue requirements
-
-## Resources
-
-### Bundled Resources
-
-**References** (in `references/`):
-- `google_scholar_search.md`: Complete Google Scholar search guide
-- `pubmed_search.md`: PubMed and E-utilities API documentation
-- `metadata_extraction.md`: Metadata sources and field requirements
-- `citation_validation.md`: Validation criteria and quality checks
-- `bibtex_formatting.md`: BibTeX entry types and formatting rules
-
-**Scripts** (in `scripts/`):
-- `search_openalex.py`: OpenAlex search client (no API key)
-- `search_pubmed.py`: PubMed E-utilities API client
-- `search_google_scholar.py`: Google Scholar search automation
-- `extract_metadata.py`: Universal metadata extractor
-- `validate_citations.py`: Citation validation and verification
-- `format_bibtex.py`: BibTeX formatter and cleaner
-- `doi_to_bibtex.py`: Quick DOI to BibTeX converter
-- `_common.py`: shared BibTeX parser, renderer, and citation-key scheme
-
-**Assets** (in `assets/`):
-- `bibtex_template.bib`: Example BibTeX entries for all types
-- `citation_checklist.md`: Quality assurance checklist
-
-### External Resources
-
-**Search Engines**:
-- OpenAlex: https://openalex.org/
-- Google Scholar: https://scholar.google.com/
-- PubMed: https://pubmed.ncbi.nlm.nih.gov/
-- PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/
-
-**Metadata APIs**:
-- OpenAlex API: https://docs.openalex.org/
-- CrossRef API: https://api.crossref.org/
-- PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/
-- arXiv API: https://arxiv.org/help/api/
-- DataCite API: https://api.datacite.org/
-
-**Tools and Validators**:
-- MeSH Browser: https://meshb.nlm.nih.gov/search
-- DOI Resolver: https://doi.org/
-- BibTeX Format: http://www.bibtex.org/Format/
-
-**Citation Styles**:
-- BibTeX documentation: http://www.bibtex.org/
-- LaTeX bibliography management: https://www.overleaf.com/learn/latex/Bibliography_management
-
-## Dependencies
-
-### Required Python Packages
-
-```bash
-uv pip install requests  # HTTP access to CrossRef, PubMed, OpenAlex, arXiv
-```
-
-BibTeX parsing, rendering, deduplication, and validation are standard library
-(`scripts/_common.py`), so `format_bibtex.py` and `validate_citations.py` run
-with no third-party packages at all.
-
-### Optional
-
-```bash
-uv pip install scholarly  # only for search_google_scholar.py
-```
-
-### Where credentials are sent
-
-This skill needs no API key. The two environment variables it reads are
-optional identifiers, each sent to the one service it belongs to and nowhere
-else; no script bundles environment variables together.
-
-| Variable | Sent only to | Purpose |
-|---|---|---|
-| `NCBI_API_KEY` | `eutils.ncbi.nlm.nih.gov` | Raises Entrez rate limits |
-| `NCBI_EMAIL` | `eutils.ncbi.nlm.nih.gov` | Entrez caller identification (requested by NCBI) |
-| `OPENALEX_EMAIL` | `api.openalex.org` | Joins the faster OpenAlex polite pool |
-
-`api.openalex.org`, `api.crossref.org`, `api.datacite.org`, `export.arxiv.org`,
-and `eutils.ncbi.nlm.nih.gov` are all queried without credentials when these are
-unset.
-
-## Summary
-
-The citation-management skill provides:
-
-1. **Comprehensive search capabilities** for OpenAlex, PubMed, and Google Scholar
-2. **Automated metadata extraction** from DOI, PMID, PMCID, arXiv ID, URLs
-3. **Citation validation** with DOI verification and completeness checking
-4. **BibTeX formatting** with standardization and cleaning tools
-5. **Quality assurance** through validation and reporting
-6. **Integration** with scientific writing workflow
-7. **Reproducibility** through documented search and extraction methods
-
-Use this skill to maintain accurate, complete citations throughout your research and ensure publication-ready bibliographies.

package/skills/clinical-decision-support/SKILL.md

@@ -1,238 +0,0 @@
----
-name: clinical-decision-support
-description: Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.
-license: MIT
-compatibility: Python 3.11+; local files only; bundled scripts use the standard library and require no network, credentials, API keys, LLMs, or image services.
-metadata:
-  version: "2.1"
-  skill-author: K-Dense Inc.
----
-
-# Clinical Decision-Support Research and Evaluation
-
-## Hard Safety Boundary
-
-This skill produces **research, evaluation, documentation, and governance artifacts only**.
-
-Never use it to:
-
-- diagnose or classify a person;
-- recommend, select, sequence, start, stop, or modify treatment;
-- calculate or communicate a patient-specific dose;
-- triage, prioritize, alarm, alert, or determine urgency;
-- make or automate a patient-specific clinical decision;
-- support bedside, point-of-care, or live clinical operation;
-- replace professional judgment or a validated, authorized clinical system;
-- claim FDA authorization, regulatory conformity, HIPAA compliance, or legal compliance.
-
-If a request could affect care for a person, stop the workflow and route the matter to a licensed healthcare professional using locally validated and appropriately authorized systems. Do not redirect to another skill for patient-specific care.
-
-## In Scope
-
-- Intended-use and limitation statements for research artifacts
-- Aggregate cohort table shells with disclosure controls
-- Statistical analysis plans and survival-analysis plan review
-- Aggregate model or biomarker performance evaluation
-- Transparent GRADE evidence-profile checklists
-- Evidence-source and decision-logic traceability
-- De-identification process checklists
-- Fairness, subgroup, calibration, uncertainty, external-validation, monitoring, change-control, audit, and human-factors documentation
-
-Outputs remain drafts until qualified humans approve them. Reporting guidance improves transparency; it does not establish study quality, clinical utility, safety, effectiveness, authorization, or compliance.
-
-## Data Gate
-
-Before any script:
-
-1. Confirm input is synthetic or aggregate.
-2. Reject patient rows, records, narratives, identifiers, free text, dates tied to people, images, waveforms, or genomic sequences.
-3. Keep source files local. Do not fetch URLs, call APIs, read environment variables, or send data to a model.
-4. Set disclosure thresholds before producing tables.
-5. Record provenance, data cut date, population, exclusions, missingness, and transformations.
-
-The scripts cap file size, groups, rows, and text length. They reject URL-like paths and common row-level keys. These controls reduce accidental misuse; they are not a privacy determination.
-
-## Required Artifact Header
-
-Every artifact must visibly include:
-
-- `artifact_type`, title, version, status, owner, date, and change summary;
-- intended purpose, intended users, aggregate population scope, and decision role;
-- all prohibited uses from the hard boundary;
-- data level and confirmation that no PHI or raw rows were supplied;
-- limitations, uncertainty, and foreseeable failure modes;
-- external-validation and subgroup applicability status;
-- human-review roles, completion status, and approval boundary;
-- source citations with versions or dates;
-- monitoring, change-control, retirement, and audit expectations;
-- the statement: **Not for patient care or live clinical use.**
-
-Start from `assets/artifact_intended_use_template.json`.
-
-## Workflow
-
-### 1. Frame the Research Question
-
-- Define the estimand or evaluation target before viewing results.
-- Distinguish descriptive, prognostic, predictive, diagnostic-accuracy, and causal questions.
-- Pre-specify outcomes, time origin, horizon, subgroups, cut points, missing-data handling, multiplicity, and sensitivity analyses.
-- Separate exploratory findings from confirmatory analyses.
-
-### 2. Select the Artifact
-
-| Need | Asset | Script |
-|---|---|---|
-| Intended-use/governance review | `assets/artifact_intended_use_template.json` | `scripts/validate_cds_artifact.py` |
-| GRADE evidence profile | `assets/evidence_profile_template.json` | `scripts/evidence_profile_check.py` |
-| Aggregate model/biomarker evaluation | `assets/aggregate_model_evaluation_template.json` | `scripts/model_biomarker_evaluation.py` |
-| Aggregate cohort table | `assets/aggregate_cohort_table_template.json` | `scripts/cohort_table_generator.py` |
-| Survival analysis plan | `assets/survival_analysis_plan_template.json` | `scripts/survival_plan_validator.py` |
-| Logic traceability matrix | `assets/decision_logic_traceability_template.json` | `scripts/decision_logic_traceability.py` |
-| De-identification process review | `assets/deidentification_checklist_template.json` | `scripts/deidentification_checklist.py` |
-
-### 3. Run Locally
-
-All helpers are dependency-free:
-
-```bash
-python3 scripts/validate_cds_artifact.py --help
-python3 scripts/evidence_profile_check.py --help
-python3 scripts/model_biomarker_evaluation.py --help
-python3 scripts/cohort_table_generator.py --help
-python3 scripts/survival_plan_validator.py --help
-python3 scripts/decision_logic_traceability.py --help
-python3 scripts/deidentification_checklist.py --help
-```
-
-Write outputs only to a reviewed local directory. Never place generated reports in an EHR, alerting system, clinical portal, or device workflow.
-
-### 4. Human Review
-
-Require review proportionate to the artifact:
-
-- methodologist/statistician for design and analysis;
-- domain expert for clinical-scientific context;
-- privacy officer or qualified expert for disclosure decisions;
-- regulatory or legal counsel for jurisdiction-specific interpretations;
-- human-factors specialist for user studies;
-- authorized governance owner for release and change control.
-
-Script success means only that declared fields and internal consistency checks passed.
-
-## GRADE Evidence Profiles
-
-Do not infer a certainty rating from article text, study design alone, p-values, or keywords. Do not use the legacy `1A/2B` shorthand as if it were universal GRADE output.
-
-For each important outcome, a human panel must document:
-
-- risk of bias;
-- inconsistency;
-- indirectness;
-- imprecision;
-- publication bias;
-- any applicable upgrading considerations;
-- effect estimate and uncertainty;
-- rationale and source IDs for every judgment;
-- final certainty judgment and named review role.
-
-The checker validates completeness and citation links only. It never calculates certainty or recommendation strength. See `references/evidence_profiles.md`.
-
-## Aggregate Model and Biomarker Evaluation
-
-Do not derive thresholds, assign molecular or disease classes, match therapies, or emit person-level predictions.
-
-The evaluator accepts only aggregate confusion counts and calibration bins. It reports bounded descriptive metrics with Wilson intervals, calibration gaps, subgroup differences, and explicit suppression. It does not determine fairness, clinical utility, or fitness for use. Require:
-
-- locked model/assay/version and pre-specified threshold provenance;
-- representative internal validation and independent external validation;
-- calibration and discrimination appropriate to the target;
-- subgroup performance with uncertainty and sample sizes;
-- missingness, spectrum/selection bias, dataset shift, and assay variability;
-- human-factors and prospective evaluation where relevant;
-- monitoring, change control, rollback, and retirement criteria.
-
-See `references/model_biomarker_evaluation.md`.
-
-## Cohort Tables
-
-Use aggregate cells only. Do not provide row-level data to the generator.
-
-- Choose the minimum cell threshold under an approved disclosure policy.
-- Apply primary and complementary suppression.
-- Report denominators and missingness.
-- Avoid baseline significance testing as a balance diagnostic.
-- Label adjusted, unadjusted, pre-specified, and exploratory results.
-- Do not interpret association as causation or clinical actionability.
-
-The default threshold is an operational safeguard, not a HIPAA rule or guarantee. See `references/cohort_evaluation.md` and `references/privacy_and_disclosure.md`.
-
-## Survival Plans
-
-Define time zero, event, competing events, censoring, intercurrent events, estimand, horizon, effect measure, and analysis population together.
-
-- Assess proportional hazards before treating a hazard ratio as constant.
-- Pre-specify alternatives such as time-varying effects or restricted mean survival time.
-- Use cumulative-incidence methods when competing events matter.
-- Address immortal-time, informative-censoring, delayed-entry, missing-data, and multiplicity risks.
-- Include sensitivity analyses and uncertainty, not only p-values.
-
-The bundled helper validates a plan; it does not analyze survival data. See `references/survival_analysis.md`.
-
-## Decision Logic
-
-Only document research or governance logic, such as evidence inclusion, validation gates, release holds, and human-review checkpoints. Each node must link to source IDs, tests, owner, version, and status.
-
-Do not encode care pathways, urgency, medication actions, diagnostic rules, alarms, or patient-facing outputs. See `references/decision_logic_traceability.md`.
-
-## Privacy and De-identification
-
-The HHS methods are Expert Determination and Safe Harbor. A checklist cannot perform either method by itself. Do not claim that removing a list of fields, hashing identifiers, using a minimum cell size, or passing this script proves de-identification or HIPAA compliance.
-
-The helper inventories documented human work. It never reads a dataset. Escalate unresolved items, free text, dates, geography, rare combinations, linkage risk, genomics, and longitudinal patterns to qualified privacy review.
-
-## Reporting-Guideline Selection
-
-- Cohort/case-control/cross-sectional: STROBE; add RECORD for routinely collected data.
-- Prediction model development/evaluation: TRIPOD+AI and PROBAST+AI.
-- Tumor prognostic marker study: REMARK.
-- AI diagnostic accuracy: STARD-AI with STARD.
-- AI trial protocol: SPIRIT-AI with the current SPIRIT base statement.
-- AI randomized trial report: CONSORT-AI with the current CONSORT base statement.
-- Early live AI evaluation: DECIDE-AI—but live evaluation is outside this skill's execution scope.
-
-These are reporting or appraisal tools, not automatic quality scores. See `references/study_reporting.md`.
-
-## Regulatory and Governance Context
-
-FDA device status turns on intended use and function, not a document label. FDA's January 2026 CDS guidance distinguishes certain non-device CDS functions from device software functions; its examples are not a self-certification checklist. ONC HTI-1 requirements apply within the defined certification scope. ICH E6(R3) and E9/E9(R1) inform trial governance and statistical planning but do not make an artifact compliant.
-
-Use `references/regulatory_and_governance.md` for dated context. Obtain qualified advice for an actual product, study, submission, deployment, or jurisdiction.
-
-## Verification
-
-From this skill directory:
-
-```bash
-python3 -m unittest discover -s tests/clinical-decision-support -p 'test_*.py'
-```
-
-Run AST compilation without bytecode:
-
-```bash
-python3 -c "import ast,pathlib; [ast.parse(p.read_text()) for p in pathlib.Path('scripts').glob('*.py')]"
-```
-
-## Reference Map
-
-- `references/README.md` — scope and navigation
-- `references/safety_and_scope.md` — refusal and escalation rules
-- `references/regulatory_and_governance.md` — FDA, ONC, ICH context
-- `references/evidence_profiles.md` — human GRADE workflow
-- `references/study_reporting.md` — EQUATOR and PROBAST+AI selection
-- `references/cohort_evaluation.md` — aggregate cohort methods
-- `references/survival_analysis.md` — time-to-event planning
-- `references/model_biomarker_evaluation.md` — model/biomarker evaluation
-- `references/privacy_and_disclosure.md` — de-identification and suppression
-- `references/decision_logic_traceability.md` — governance logic
-- `references/sources.md` — dated authoritative source ledger
-- `references/security_validation.md` — scan results and accepted LOW findings

package/skills/clinical-decision-support/references/README.md

@@ -1,62 +0,0 @@
-# Clinical Decision-Support References
-
-Version 2.0 is the breaking safety redesign dated 2026-07-23. It replaces
-the former recommendation-oriented templates, references, and scripts with
-offline research-evaluation and governance artifacts.
-
-## Boundary
-
-These references support aggregate or synthetic research evaluation, methods documentation, evidence profiles, privacy review, and governance traceability. They do not support diagnosis, treatment recommendations, dosing, triage, alarms, bedside use, autonomous decisions, or patient-specific output.
-
-No reference or script establishes regulatory authorization, HIPAA compliance, clinical validity, or fitness for live use. Route care decisions to licensed professionals using validated and appropriately authorized systems.
-
-## Navigation
-
-| File | Purpose |
-|---|---|
-| `safety_and_scope.md` | Refusal rules, escalation, and intended-use language |
-| `regulatory_and_governance.md` | FDA CDS/AI, ONC HTI-1, and ICH context |
-| `evidence_profiles.md` | Human GRADE evidence-profile workflow |
-| `study_reporting.md` | STROBE/RECORD, TRIPOD+AI, CONSORT-AI, SPIRIT-AI, DECIDE-AI, STARD-AI, REMARK, and PROBAST+AI |
-| `cohort_evaluation.md` | Aggregate cohort reporting and disclosure-aware tables |
-| `survival_analysis.md` | Estimand-led time-to-event planning |
-| `model_biomarker_evaluation.md` | Aggregate validation, calibration, uncertainty, and subgroup review |
-| `privacy_and_disclosure.md` | HHS de-identification methods and output controls |
-| `decision_logic_traceability.md` | Research/governance logic matrices |
-| `sources.md` | Authoritative source ledger checked 2026-07-23 |
-| `security_validation.md` | Baseline remediation, scan results, and accepted LOW findings |
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-## Assets
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-All assets are JSON skeletons. They contain no patient rows or real identifiers:
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-- `artifact_intended_use_template.json`
-- `evidence_profile_template.json`
-- `aggregate_model_evaluation_template.json`
-- `aggregate_cohort_table_template.json`
-- `survival_analysis_plan_template.json`
-- `decision_logic_traceability_template.json`
-- `deidentification_checklist_template.json`
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-Every template includes intended use, prohibited uses, limitations, data level, and human-review fields.
-
-## Scripts
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-The standard-library scripts read bounded local JSON and produce bounded local JSON, Markdown, or CSV:
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-- `validate_cds_artifact.py`
-- `evidence_profile_check.py`
-- `model_biomarker_evaluation.py`
-- `cohort_table_generator.py`
-- `survival_plan_validator.py`
-- `decision_logic_traceability.py`
-- `deidentification_checklist.py`
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-They do not use networks, API keys, environment variables, dynamic evaluation, serialization formats that execute code, LLMs, or image services.
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-## Method Selection
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-Use the study design and evaluation stage—not the presence of “AI” in a title—to select a framework. Reporting checklists are minimum disclosure guidance. Risk-of-bias tools require informed human judgments. GRADE certainty is outcome-specific and cannot be inferred from text.
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-For an actual protocol, product, regulated submission, certified health IT module, or data release, obtain review from the relevant methodologist, privacy official, legal/regulatory counsel, governance owner, and domain experts.
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