/manuscript-provenance

name: manuscript-provenance
description: 'Computational provenance audit verifying every number, table, and figure in a manuscript derives from code, not manual entry. Triggers on: "check provenance", "verify reproducibility", "audit my pipeline", "are my numbers from code", "provenance audit". Companion to manuscript-review (prose audit).'
metadata:
  version: 1.2.0
  complements:
    [
      manuscript-review,
      manuscript-typography,
      figure-rhetoric,
      figure-table-quality,
      arxiv-preflight,
    ]
  category: review
  tags: [provenance, reproducibility, computational, verification]
  difficulty: advanced
  phase: review

Manuscript Provenance Audit

**Pipeline position:** Phase 2a (grounding audit). Runs in parallel with `manuscript-typography`. Depends on: content settled after Phase 1 fixes. Produces macro manifest consumed by `manuscript-review` Pass 13 (Cross-Element Coherence).

Purpose

Verify that a manuscript is a faithful rendering of computational outputs. Every number, table, figure, category label, ordering, and threshold in the document must trace to a specific script, config file, or pipeline output. Manual data entry in a manuscript is a reproducibility defect.

This skill produces a provenance map — a structured report linking each manuscript artifact to its generating code — and flags every break in the chain.

Companion skill: `manuscript-review` audits the document as prose (structure, argumentation, citations). This skill audits whether the document content is computationally grounded. Run both for complete pre-publication coverage.

Boundary Agreement with manuscript-review

| Concern | manuscript-review | This skill (manuscript-provenance) | | ------------------------- | ----------------------------------------------------------- | -------------------------------------------------------------- | | Reproducibility | Does the paper describe enough to reproduce? (§6) | Does the code actually produce what the paper claims? (§1, §7) | | Figures/Tables | Legible, accessible, well-formatted? (§12) | Generated by scripts, not manual entry? (§2, §3) | | Rendered visuals | Readable at print scale? Floats near references? (§23) | Figure generation script produces correct format? (§3) | | Hyperparameters | Listed in the paper with rationale? (§6) | Values trace to config files, not hardcoded? (§1, §8) | | Code availability | Statement exists in the paper? (§17) | Repo URL valid, README accurate, pipeline works? (§11) | | Terminology | Abbreviations consistent within document? (§14) | Terms match code identifiers? (§5) | | Significant figures | Consistent precision within document? (§12) | Precision matches script output? (§2) | | Figure format | Appropriate format for document quality? (§12) | Format generated by script, not manually exported? (§3) | | Computational cost | Reported in the paper? (§7) | Values trace to benchmarking scripts? (§1) | | Macro-prose coherence | Prose framing appropriate for injected value? (§24) | Value traced to code, macro manifest produced? (§4) | | Cross-element consistency | Prose, captions, figures, tables mutually consistent? (§24) | All elements from same run/pipeline output? (§9) |

**Rule:** This skill never judges prose quality. manuscript-review never opens the codebase. Each reads the other's report when available.

**Integration point — Macro Manifest:** This skill produces a **macro manifest** as part of the §4 audit: a structured list of every macro-injected value with:

• Macro name (e.g., `\bestf`)
• Resolved value (e.g., `0.847`)
• Source (script + output file that generates it)
• Location(s) in manuscript text (file, line number, surrounding sentence)
• Classification (TRACED / MACRO-TRACED / CONFIG-TRACED / UNTRACED / STALE)

manuscript-review's Pass 13 (Cross-Element Coherence, §24) consumes this manifest to check whether the prose surrounding each injected value is appropriate for the actual numeric value. Provenance owns "is this value computationally grounded?" Review owns "does the text wrapping this value make sense given what the value is?"

Scope

**In scope:**

• Numbers, metrics, percentages in manuscript text
• Tables (content, ordering, formatting)
• Figures (generation scripts, data sources)
• LaTeX macros (`\newcommand`, `\def`, `\pgfmathsetmacro`)
• Terminology, mode names, mechanism labels, category names
• Ordering of items in enumerations, tables, discussion
• Config values (thresholds, hyperparameters, model names)
• Pipeline completeness (raw data → final PDF)
• Timestamp consistency (scripts vs outputs)

**Out of scope:**

• Prose quality (→ manuscript-review)
• Citation hygiene (→ manuscript-review)
• Argumentation structure (→ manuscript-review)
• Code quality/style (separate concern)

Inputs

This audit requires TWO artifacts:

1. **Manuscript source** — LaTeX `.tex` files (preferred), or PDF/DOCX as fallback 2. **Codebase** — the scripts, configs, and pipeline that generate manuscript content

If the user provides only one, ask for the other. LaTeX source is strongly preferred over compiled PDF — provenance auditing requires seeing the raw markup, macros, and input commands.

Workflow

Phase 1 — Inventory

**1a. Manuscript Artifact Extraction**

Read all `.tex` files (main + included via `\input`/`\include`). Extract:

• **Inline values**: bare numbers in running text (percentages, counts, metrics,

p-values, confidence intervals, thresholds, sizes)

• **LaTeX macros**: all `\newcommand