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

bash

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

bash

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

bash

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

bash

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

Required CSV headers:

text

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:

text

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

The audit also flags numeric content without a claim marker.

Numeric and methods-results consistency

bash

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

bash

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

bash

python3 scripts/validate_authorship.py authorship.json

The command checks human authorship criteria, exact CRediT role names, corresponding author and guarantor IDs, final approval, hashed declarations, AI disclosure, human verification, journal-policy review, and authorization gates for restricted material.

Language, placeholder, and confidentiality lint

bash

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.