Local CLI Reference

All bundled commands use only the Python standard library. They:

• accept explicit UTF-8 JSON, CSV, or Markdown files;
• reject symbolic-link inputs;
• cap file size, records, fields, JSON nodes, and nesting;
• make no network calls;
• read no environment variables or .env files;
• perform no dynamic evaluation or pickle loading;
• report issue codes, IDs, and line numbers without echoing manuscript or source text.

Run from the skill directory with Python 3.11 or newer.

Scaffold

python3 scripts/scaffold_manuscript.py \
  --output-dir ./draft-workspace \
  --document-id local-draft \
  --study-design randomized_trial \
  --guideline consort-2025

The output directory must not exist. The command never overwrites files. Generated documents are explicitly incomplete and not submission-ready.

Manifest validation

python3 scripts/validate_manifest.py manuscript_manifest.json --kind manuscript
python3 scripts/validate_manifest.py source_manifest.json --kind source
python3 scripts/validate_manifest.py source_manifest.json --kind source --require-verified

The validator checks structure, IDs, verification gates, confidentiality status, and required-statement status. It does not read files named inside the manifest.

Reporting-guideline routing and coverage

python3 scripts/select_reporting_guidelines.py select --study-design systematic_review
python3 scripts/select_reporting_guidelines.py check reporting_coverage.json

Selection and coverage are non-scoring. Open the official guideline after selection.

Claim and citation audit

python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json

Required CSV headers:

claim_id,section,claim_kind,claim_text_sha256,evidence_ids,verification_status,uncertainty,analysis_intent

Separate multiple evidence IDs with semicolons in CSV. Use inline Markdown markers:

[claim:C001] [evidence:E001,E002]

Use exactly one claim per physical line. The audit checks the SHA-256 digest against that line after removing [claim:...], [evidence:...], and [@E...] markers and collapsing whitespace. It also validates source-manifest verification metadata and flags numeric content without a claim marker. See evidence_workflow.md for normalization and limits.

Numeric and methods-results consistency

python3 scripts/check_consistency.py consistency_manifest.json

The command checks duplicate concepts across sections, units, percentages against numerators and denominators, sample sizes, evidence IDs, declared methods, outcome mappings, and confirmatory or exploratory status.

Reference identifiers and duplicates

python3 scripts/check_references.py source_manifest.json

The command checks local syntax and duplicates for DOI, PMID, PMCID, ISBN, URL, and normalized title. It never resolves an identifier; a human must compare each value with the opened source.

Authorship and disclosure

python3 scripts/validate_authorship.py authorship.json

The command checks human authorship criteria, exact CRediT role names, corresponding author and guarantor IDs, final approval, declaration-hash syntax, AI disclosure, human verification, journal-policy review, and authorization gates for restricted material. Its authorship criteria are ICMJE-style local gates, not all journals' criteria. Declaration hashes are not compared with manuscript text; manually reconcile the actual statements. Recorded dates must be valid calendar dates in YYYY-MM-DD form.

Language, placeholder, and confidentiality lint

python3 scripts/lint_manuscript.py manuscript.md \
  --manifest manuscript_manifest.json

Possible sensitive-content findings are review prompts, not a de-identification certificate. The linter intentionally fails on unresolved placeholders.

Exit behavior

• exit 0: no error-level findings;
• exit 1: invalid input or one or more error-level findings.

Warnings still require human review. JSON output is deterministic for the same inputs.