# Manuscript Review > Pre-publication manuscript audit producing a section-level refactoring report with citation hygiene and submission-readiness checks. Triggers on: "review my paper", "check before submission", "is this ready to submit", "pre-pub checklist", "refactor my paper", "check my references", "does the abstract work". - **Type:** Skill - **Install:** `agentstack add skill-mathews-tom-armory-manuscript-review` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [Mathews-Tom](https://agentstack.voostack.com/s/mathews-tom) - **Installs:** 0 - **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [Mathews-Tom](https://github.com/Mathews-Tom) - **Source:** https://github.com/Mathews-Tom/armory/tree/main/skills/manuscript-review - **Website:** https://mathews-tom.github.io/armory/ ## Install ```sh agentstack add skill-mathews-tom-armory-manuscript-review ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About # Manuscript Review Skill **Pipeline position:** Phase 1a (content audit). Runs in parallel with `figure-rhetoric`. No prior dependencies. Outputs consumed by `manuscript-provenance` (macro manifest feedback) and `figure-rhetoric` (claims map for visual argument assessment). See companion skills for full pre-publication coverage: `manuscript-typography` (typographic conventions), `citation-audit` (citation truth), `arxiv-preflight` (submission compliance). ## Purpose Execute a comprehensive, multi-pass diagnostic audit of an academic or technical manuscript, producing a structured improvement report that identifies issues across 24 audit dimensions — from macro-coherence and argumentative architecture through claims-evidence calibration, narrative flow, prose microstructure, rendered visual inspection, and cross-element coherence, down to citation hygiene and reproducibility. The output is a prioritized, actionable improvement plan — not a line edit. The goal is to surface structural, logical, and clarity issues that authors systematically miss because they're too close to the text. Optimized for arXiv/preprint submissions with flexible compliance standards. Companion skill: `manuscript-provenance` audits whether manuscript content (numbers, tables, figures, ordering, terminology) is computationally derived from code and scripts. This skill audits the document as prose; that skill audits computational grounding. Run both for complete pre-publication coverage. ## Boundary Agreement with manuscript-provenance | Concern | This skill (manuscript-review) | 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 opens the codebase. manuscript-provenance never judges prose quality. Each reads the other's report when available. **Integration point — Macro Manifest:** manuscript-provenance produces a **macro manifest** as part of its §4 audit: a structured list of every macro-injected value, its resolved numeric value, its source (script + output file), and its location(s) in the manuscript text. This skill's Pass 13 (Cross-Element Coherence) consumes that manifest to check whether the prose surrounding each injected value is appropriate for the actual value. If no provenance report exists, this skill extracts macro values directly from `.tex` source (less precise — no source tracing, but coherence check still runs). ## Workflow ### 1. Ingest Read the uploaded manuscript. Accept PDF, DOCX, LaTeX source, or Markdown. If multiple files are uploaded (e.g., main text + supplementary), process all of them. Identify: - Target venue (defaults to arXiv/preprint; adjust if conference/journal submission) - Submission type (full paper, technical report, thesis chapter, etc.) - Any specific concerns the user raised — these get priority in the report For arXiv submissions, compliance checks are advisory. Focus on technical quality, reproducibility, and clarity rather than strict formatting rules. ### 2. Load the Checklist Read `references/checklist.md` — the comprehensive 24-section, ~175-checkpoint refactoring checklist. Every audit pass is structured against this checklist. ```text Read references/checklist.md ``` ### 3. Multi-Pass Audit Execute the following passes sequentially. Each pass maps to one or more checklist sections. Work systematically — for each checkpoint: - **PASS**: Note briefly, move on - **FAIL**: Document with exact location (section, paragraph, line), specific defect, concrete fix required - **N/A**: Mark if not applicable to this manuscript type **Pass 1 — Structural Integrity (Checklist §1, §4, §5, §10)** - Trace the thesis-thread from abstract through conclusion - Verify section-level necessity and logical dependency ordering - Check introduction funnel structure and contribution enumeration - Verify conclusion contains no new information and maps 1:1 to stated contributions - Assess related work organization (taxonomic vs. annotated) and differentiation **Pass 2 — Abstract & Title Calibration (Checklist §2, §3)** - Abstract functional completeness (context → gap → approach → results → implication) - Quantitative specificity in abstract - Title precision-scope alignment - Keyword-abstract coherence **Pass 3 — Technical Rigor (Checklist §6, §7)** - Reproducibility sufficiency of methodology (document-level: does the paper describe enough? Code-level verification deferred to manuscript-provenance) - Assumption explicitness and notation consistency - Baseline adequacy, dataset characterization, statistical rigor - Effect size reporting, evaluation metric justification - Computational cost reporting (checks paper reports it; value tracing to benchmarking scripts deferred to manuscript-provenance) **Pass 4 — Argumentation Quality (Checklist §8, §9)** - Discussion introduces no new results - Alternative explanations considered - Generalizability boundaries stated - Limitations genuine (not performative), preemptively addressing reviewer objections - Threat-to-validity taxonomy coverage **Pass 5 — Citation & Reference Hygiene (Checklist §11)** - Citation-reference bijection (no orphans in either direction) - Style conformance to target venue - Primary source preference over secondary citations - Preprint-to-publication status check - Citation placement (claim-level, not paragraph-level) - Retraction check advisory **Pass 6 — Visual & Tabular Quality (Checklist §12)** - Sequential callout ordering - Resolution and legibility assessment - Colorblind accessibility - Axis labels with units, consistent visual language - Table alignment and significant figure consistency **Pass 7 — Prose Mechanics (Checklist §13, §14, §15)** - Tense consistency (recommendations, not strict requirements) - Hedging calibration (neither overclaiming nor vacuous) - Passive voice patterns (advisory) - Nominalization reduction opportunities - Clarity and precision (marketing language advisory for arXiv) - Abbreviation hygiene (first-use expansion, consistency) - Mathematical typesetting consistency **Pass 7b — AI-Pattern Detection (advisory)** Scan prose sections for residual AI-writing patterns using detection rules from `references/detection-patterns.md`. Academic manuscripts drafted or polished with AI assistants often retain detectable tells. Focus on patterns relevant to academic writing: - Significance inflation (#1) — "pivotal", "groundbreaking", "paradigm shift" - AI-frequency vocabulary (#7) — "delve", "landscape", "tapestry", "underscore" - Copula avoidance (#8) — "serves as" instead of "is" - Vague attributions (#5) — "experts argue", "studies have shown" without citations - Filler phrases (#22) — "it is important to note that" - Excessive hedging (#23) — beyond what epistemically appropriate hedging requires Skip patterns that are acceptable in academic prose: - Passive voice — standard in methods sections - Formal transitions — "Furthermore", "Moreover" are conventional in academic writing - Title case headings — journal style may require it This pass is MEDIUM priority. Flag findings but do not over-correct — academic conventions overlap with some AI patterns. Severity: report individual instances as LOW, flag clusters of 3+ patterns in a single paragraph as MEDIUM. **Pass 8 — Best Practices & Reproducibility (Checklist §16, §17, §18, §19)** - Supplementary material cross-reference integrity - Code/data availability statements exist in the paper (verification that claimed repos are valid and pipelines work deferred to manuscript-provenance) - License compatibility for third-party assets - Hyperlink verification and reference integrity - Overall clarity and accessibility assessment **Pass 9 — Claims-Evidence Calibration (Checklist §20)** This is a dedicated pass through every assertion in the manuscript. For each claim: 1. Grade claim strength: strong/definitive ("X causes Y"), moderate/qualified ("X improves Y under conditions Z"), or hedged/tentative ("X may contribute to Y") 2. Grade evidence strength: direct experimental, indirect/correlational, citation-only, analogical, or no evidence 3. Flag mismatches: - **Overclaim**: Strong claim + weak evidence → soften the claim or add evidence - **Underclaim**: Hedged language + strong evidence → sharpen the language - **Orphaned claim**: Any strength + no evidence → add evidence or remove claim 4. Audit causal vs. correlational language against study design 5. Check generalization scope against actual experimental conditions 6. Verify comparative claims ("outperforms", "better than") against head-to-head evaluations actually present in the paper 7. Flag implicit claims (e.g., "Unlike prior work, our approach handles X" implies prior work cannot — verify this) 8. Check negation claims for evidence of absence vs. absence of evidence This pass is HIGH priority. Claims-evidence mismatch is the single most common reason reviewers reject papers. An overclaim in the abstract poisons the entire reading. **Pass 10 — Narrative Flow & Coherence (Checklist §21)** Read the manuscript linearly, tracking the reader's cognitive state. At each sentence and paragraph boundary, check: - Does this sentence follow from the previous one, or does the reader need to make an inferential leap? - Does this paragraph's opening sentence state its point, or is the point buried? - Does each sentence start with known information and end with new information (given-new contract)? - Are cross-references between sentences ordered so the reader moves forward through the text, not zigzagging back? - Does the last sentence of each paragraph connect to the first sentence of the next paragraph? - Are there logic gaps where a premise is skipped because the author knows it implicitly? - Does every setup/promise within a section get its payoff within that section? - Does each section have a discernible arc (setup → content → landing)? Flag any location where a domain-expert reader would need to re-read, scroll back, or pause to reconstruct the logical connection. These are flow breaks. This pass is HIGH priority. Papers with strong results but poor narrative flow exhaust reviewers. A reader who has to fight the text stops trusting the author. **Pass 11 — Prose Microstructure (Checklist §22)** Sentence-level and paragraph-level patterns that compound into readability problems: - Ambiguous referents: "this", "it", "they" without clear antecedents - Information density spikes: paragraphs introducing too many new concepts at once - Sentences requiring multiple re-reads: excessive clause nesting, misplaced modifiers, garden-path constructions - Broken parallel structure in lists, comparisons, sequences - Semantic redundancy: same point restated in nearby paragraphs without purpose - Long-distance references: concepts introduced and referenced many paragraphs later without re-anchoring - Dangling modifiers: "Using gradient descent, the loss function converged" This pass is MEDIUM priority on individual items but compounds — a manuscript with 20 ambiguous pronouns, 10 density spikes, and 5 dangling modifiers is materially harder to read even though no single instance is fatal. **Pass 12 — Rendered Document Inspection (Checklist §23)** This pass requires the compiled PDF. If only LaTeX source is provided, ask the user for the compiled PDF or compile it. Open the PDF and inspect every page at actual print scale: 1. **Figures**: For each figure, zoom to the size it will appear at in the final document. Check: - All text (axis labels, tick labels, legend, annotations) readable - No label overlap, collision, or truncation - Legend placement not covering data - Annotations pointing to correct elements 2. **Tables**: Check column alignment, text wrapping, no content overflow 3. **Floats**: For each figure/table, locate its first text reference. Measure the page distance. Flag anything >1 page away. 4. **Page breaks**: Check no table splits across pages (unless intentionally long), no equation orphaned from its introduction, no header stranded at page bottom 5. **Margins**: Check no content bleeds outside margins (equations, URLs, wide tables, wide figures) 6. **Visual consistency**: Font sizes across figures comparable, color usage consistent This pass is HIGH priority. A paper with illegible axis labels or a table split across pages signals carelessness to reviewers regardless of technical quality. These defects are invisible from source and the author often doesn't notice because they read the paper in their editor, not in the compiled output. **Pass 13 — Cross-Element Coherence (Checklist §24)** Read the manuscript as an integrated system. For each figure, table, and macro-injected value: 1. **Collect the element cluster**: The visual/data itself, its caption, every prose passage that references it, and any macro values appearing in or near those passages 2. **Check four-way consistency**: Does the prose claim match the visual? Does the caption describe the current content? Do the numbers agree across text, table, and figure? Does the qualitative language match the quantitative values? 3. **Check cross-reference accuracy**: Every `\ref` points to the element the surrounding prose describes. After figure reordering, references often point to the wrong visual. 4. **Check macro-prose coherence**: When a macro injects a number, read the sentence it sits in. Does the qualitative framing ("modest", "dramatic", "marginal", "substantial") match the actual numeric value? This is the handoff from manuscript-provenance: provenance traces the value to code, this pass verifies the prose wrapping that value is appropriate. 5. **Check temporal consistency**: Do all elements appear to come from the same experimental run? A figure from one run and a table from another is a coherence failure even if both are individually correct. If a manuscript-provenance report exists, load its macro manifest (list of all traced macro values wit … ## Source & license This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code. - **Author:** [Mathews-Tom](https://github.com/Mathews-Tom) - **Source:** [Mathews-Tom/armory](https://github.com/Mathews-Tom/armory) - **License:** MIT - **Homepage:** https://mathews-tom.github.io/armory/ Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/skill-mathews-tom-armory-manuscript-review - Seller: https://agentstack.voostack.com/s/mathews-tom - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. 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