Init
Conversationally bootstrap MANUSCRIPT_STATE.yaml for a new or existing manuscript directory. Infers what it can from the filesystem (title, sections, bibliography paths) and asks the author about the subjective fields (core_claims, known_weaknesses, terminology, audience). Validates against the JSON Schema before writing. Invoke when the user wants to set up scriptorium on a manuscript that does…
Citation Audit
Audit existing citations in a manuscript for claim-support alignment, primary-vs-review mismatch, causal overreach, and unsupported assertions. Reports findings as structured markdown. Does NOT add or invent citations.
Reporting Guideline Compliance
Run an EQUATOR Network reporting-guideline checklist (CONSORT, STROBE, PRISMA, ARRIVE, STARD, TRIPOD/TRIPOD+AI, CARE, COREQ, CHEERS, plus AI extensions) against a manuscript and classify every checklist item as present / partial / missing / not-applicable. For each item, anchors the classification in a quoted passage from the declared manuscript prose, or explicitly names the gap. Downstream of t…
Gap Finder
Identify gaps in existing draft prose — claims under-supported, premises missing, related work not engaged with, counterarguments not addressed, internal-consistency mismatches — and suggest directions for filling them. Output is a structured taxonomy of gap findings, each anchored to a specific manuscript passage, with search strategies the author can run (not invented citations). Refuses cleanl…
Argumentative Flow
Improve a manuscript section's logical and argumentative coherence while preserving every citation, statistic, and declared terminology choice. Produces a structural diagnosis, a proposed outline, the revised text with a diff against the source, and a preservation report. Invoke ONLY when the user explicitly asks for argumentative-flow improvement on a specific section.
Terminology Normalization
Detect terminology drift across a manuscript and enforce the preferred / forbidden / synonyms lists declared in MANUSCRIPT_STATE.yaml. Reports inconsistencies with exact occurrence locations and suggests normalizations. Does NOT modify the manuscript without explicit author consent.
Desk Rejection Risk
Author-side pre-submission audit that flags triggers likely to result in desk rejection before peer review — scope/audience mismatch, format and length issues, missing or weak required sections, weak significance framing, and presentation problems editors triage on. Outputs a structured markdown report with a qualitative risk band. NOT for editorial-side use — running this on someone else's manus…
Reporting Guideline Fit
Read the manuscript's methods section (and abstract/title for context) and infer which EQUATOR Network reporting guideline applies — CONSORT for RCTs, STROBE for observational, PRISMA for systematic reviews, ARRIVE for animal research, TRIPOD/TRIPOD+AI for prediction models, STARD for diagnostic accuracy, CARE for case reports, COREQ for qualitative, with relevant AI-extensions (CONSORT-AI, SPIRI…
Figure Text Alignment
Audit text-only alignment between figure captions and the body-text sentences that reference them. For every figure, classify the caption ↔ body-text-reference pair as aligned / partially aligned / misaligned / cannot determine, and flag pattern-level issues (orphan figure, phantom figure, panel mismatch, axis/units divergence, direction divergence). This is the text-only subset of figure-text al…
Venue Fit
Assess venue fit for a manuscript and return a tiered set of candidate venues (likely fit / stretch / probably premature) with per-venue rationale, fit caveats per axis (scope, audience, methodological, novelty, significance, open-access/cost), and explicit predatory-venue refusal. Handles three author states — decided (assesses target_venue and offers alternatives), considering (assesses each de…
Compression
Propose page-limit-driven length reductions on a manuscript section while preserving every citation, every declared statistic, every core claim, and every declared terminology choice. Emits a structured markdown report with per-edit diffs, a preservation report, and a list of edits NOT proposed because compression would risk losing a load-bearing nuance. Suggests edits; never auto-applies. Invoke…
Outlier Sentence Detector
Flag sentences that are statistical outliers in the manuscript along three narrow dimensions — length, syntactic complexity, and nominalization density — for human review. Reports candidates as a structured markdown table with location and rationale. Does NOT produce a quality score, a grade, or a pass/fail. Does NOT edit the manuscript. Calibrates against the manuscript's own distribution so the…
Reviewer Simulation
Author-side simulation of peer review across four attentional lenses (methodological skeptic, domain expert, translational/clinical, statistical). Surfaces likely major and minor critiques, fatal concerns, enthusiasm drivers, and concrete revision suggestions. Output is structured markdown. NOT for editorial-side use — running this on someone else's manuscript violates ICMJE / NIH / Elsevier / Na…
Tour
Conversational onboarding for new users. Three or four turns. Greets, asks what the user is working on (manuscript, grant, review, or exploring), walks through the relevant subset of scriptorium, shows an example MANUSCRIPT_STATE.yaml, and ends with a concrete next move (usually scriptorium:init). Does no work on the user's project — strictly read-only. Designed to be the single skill a maintaine…
Explain
Explain scriptorium itself, a named skill, or a named MANUSCRIPT_STATE field. With no argument, gives a whole-system overview (what scriptorium is, what each skill does, how the shared state ties them together). With an argument, drills into that skill or field — what it does, what it consumes, what it produces, and the grounding notes behind its design. Reads SKILL.md frontmatter and the referen…
Author Contribution Audit
Audit the manuscript's Author Contributions section against ICMJE's four authorship criteria and CRediT's 14 contributor roles. Flag what's missing per author, suggest how to map who-did-what to canonical CRediT roles, and (when `target_venue` is set) compare against journal-specific variants. Operates on the declared Author Contributions section in the manuscript — does not duplicate authorship…