/audit — Thesis Consistency Audit Skill

Running Python helpers

Choose the interpreter before running the examples. For a globally installed copy, use the private runtime recorded by its installer. In a checkout or linked workspace, use AWT_PYTHON when set, otherwise the toolkit's .venv (follow the skill directory link back to the toolkit): Scripts/python.exe on Windows, bin/python on macOS/Linux. Without that environment, check that python (Windows) or python3 (macOS/Linux) actually runs and has the helper's dependencies. Replace the example's python3 with that executable. In PowerShell, prefix a quoted executable with &; keep commands on one line and quote file paths.

Purpose

Scan all thesis chapters for internal data consistency issues: contradictory numbers, inconsistent terminology, broken cross-references, and arithmetic errors. This is a pre-submission quality check.

Trigger Words

This skill activates on: audit, consistency check, check numbers, /audit.

Workflow

1. Scan all chapter files in the chapters/ directory using Glob. Read each file to extract quantitative claims, terminology, and cross-references.

2. Check the following categories:

   A. Numerical consistency

   • The same statistic (e.g., accuracy, sample size, p-value) cited in multiple chapters must have the same value.
   • Percentages in a distribution must sum to 100% (with tolerance of +/-1% for rounding).
   • Counts (e.g., "42 models") must match between chapters.

   B. Terminological consistency

   • The same concept must use the same term throughout. Flag cases where synonyms are used inconsistently (e.g., "structured review" vs "systematic review" for the same concept).
   • Abbreviations must be defined on first use in each chapter.

   C. Cross-reference validity

   • References to other sections (e.g., "as discussed in Section 3.2") must point to sections that exist.
   • References to tables and figures must match actual table/figure numbers.
   • Forward references ("Chapter 6 will show...") must be fulfilled.

   D. Citation checks — disabled in this release (disclosed gap)

   The deterministic citation tiers previously run here are disabled: measured against realistic thesis text they produced false high-severity "phantom citation" findings on ordinary parentheticals, missed multi-word institutional authors, and flagged the comma form that Cite Them Right Harvard mandates. Until the checker meets a measured, disclosed false-positive rate, do not run it and do not present citation consistency as audited. Reference integrity is still covered by /verify-refs (BibTeX records) and by the notes-file contract lint.

   E. Claim positioning (deterministic, runs before F and G — positioning is not repairable after review; style is)

   python3 .claude/skills/audit/scripts/audit-claim-positioning.py --base-dir chapters --bib references.bib --json
   

   (omit --bib when the project has no bibliography file). Report every issue it returns: unsourced-keyword and bare-novelty as High — a field's vocabulary in use without its literature, or a novelty claim in a paragraph that shows no search — uncited-method and dangling-entry as Medium. The tool checks that a source is present near a claim, never that it is the right one, and it cannot tell whether a citing sentence says what its source says; do not present its silence as either.

   For a requested claim-scope or contribution review, consult references/argument-licence/argument-level-lock.md. Separate the field gap, delivered contribution, observed finding and extrapolation; report the six-line claim licence and any unsupported transition with a text or evidence anchor. This is an Advisory reading task. Do not create standing CSV ledgers or infer scientific validity from a checker result. Existing legacy packets can be interpreted with the schema and checks linked in references/argument-licence/README.md.

   F. Citation fidelity — does the citing sentence match its source?

   node .claude/skills/audit/scripts/audit-citation-fidelity.mjs --base-dir . --json
   

   (needs the guards built once: npm --prefix guards install && npm --prefix guards run build.) Report quote-not-in-source and page-mismatch as High — a quoted span that is not verbatim in the source's notes or PDF, or a page that the source contradicts — and notes-missing as Medium. low-overlap is experimental: list it under Measurements as a prompt to re-read, never as an issue; no false-positive rate has been measured for it yet. State the tool's own limit in the report verbatim: it does not detect a sentence that inverts its source in the source's own words — the failure that mattered most on a real manuscript — and that still requires reading. Every finding here is a proxy; a finding is a reason to open the source, not a verdict.

   G. Prose fingerprint (measurement only; skip when no baseline exists)

   Only when the project holds a baseline corpus of its own reference PDFs (literature/, twenty or more, the author's own papers excluded):

   python3 .claude/skills/audit/scripts/audit-prose-fingerprint.py --target chapters --baseline literature --exclude '<author-surname>*'
   

   Report the distributions under Measurements, never as issues: this is Advisory by nature. Out-of-range is the hard signal, a percentile is a soft one, and clustering matters more than count. Method and stop rules: references/prose-polish-method.md.

3. Output the audit report using the format below.

Output Format

## Audit Report -- {YYYY-MM-DD}

### Summary

- **Critical**: {N} issues (contradictory data)
- **High**: {N} issues (broken references, missing definitions)
- **Medium**: {N} issues (terminology inconsistency, minor arithmetic)

### Issues

| # | Severity | Category | Location | Issue | Current | Expected |
|---|----------|----------|----------|-------|---------|----------|
| 1 | Critical | Numerical | Ch3 s3.2, Ch5 s5.4 | Sample size differs | 120 (Ch3) vs 125 (Ch5) | Should be consistent |
| 2 | High | Cross-ref | Ch4 s4.1 | Ref to "Section 3.7" | Section 3.7 | Section does not exist |

### Measurements (category G when a baseline exists; category F's experimental low-overlap prompts)

{Per metric: rate, clustering (gap CV), longest gap — with the baseline's
range and where the manuscript sits. Numbers, not verdicts.}

### Recommendations

{Grouped by severity, brief notes on how to resolve each issue.}

Severity Levels

• Critical: The same quantitative claim has different values in different chapters. This directly undermines thesis credibility.
• High: Broken cross-references, undefined abbreviations on first use, missing table/figure numbers.
• Medium: Inconsistent terminology that does not cause factual error, minor rounding discrepancies within tolerance.

Constraints

1. Never auto-fix. List all issues for the user to review and decide. The user may choose to fix selectively.
2. No emoji in output.
3. Report all instances, not just the first occurrence. If a statistic appears in 4 chapters with 2 different values, list all 4 locations.
4. Be specific about locations. Provide chapter number, section number, and surrounding context so the user can find the issue quickly.
5. Do not flag stylistic issues. This skill checks data consistency, not prose quality.