---
id: manuscript-architect
stage: F_writing
description: "Build coherent paper structure from outline to section-level drafts with claim-evidence integrity and analysis-depth checking."
inputs:
  - type: RQSet
    description: "Research questions"
  - type: EvidenceTable
    description: "Synthesized evidence"
  - type: DesignSpec
    description: "Study design (for empirical or qualitative papers)"
    required: false
outputs:
  - type: ManuscriptOutline
    artifact: "manuscript/outline.md"
  - type: Manuscript
    artifact: "manuscript/manuscript.md"
  - type: ClaimGraph
    artifact: "manuscript/claims_evidence_map.md"
  - type: FiguresTablesPlan
    artifact: "manuscript/figures_tables_plan.md"
constraints:
  - "Must maintain claim-evidence alignment across sections"
  - "Must follow venue-specific sectioning requirements"
  - "Every section must have an explicit analytical job"
failure_modes:
  - "Evidence gaps discovered during writing"
  - "Scope creep from unfocused claims"
  - "Discussion that merely restates results without interpretation"
tools: [filesystem]
tags: [writing, manuscript, outline, drafting, claim-evidence]
domain_aware: true
---

# Manuscript Architect Skill

Build and revise a full research paper manuscript across stages: outline → section drafts → coherence pass → compliance checks → submission-ready package.

## Purpose

Build coherent paper structure from outline to section-level drafts with claim-evidence integrity and analysis-depth checking.

## When to Use

- You want to draft a paper from an existing `RESEARCH/[topic]/` project folder (empirical study or systematic review).
- You want to draft a fully qualitative paper from interview, case, ethnographic, or document-based materials without defaulting back to a quantitative structure.
- You have partial materials (notes, tables, analysis plan, results) and want a coherent manuscript.

## Granularity Boundary

Keep these as embedded writing subflows inside `manuscript-architect` unless they own a separate contract artifact:

- story spine construction
- section-level drafting
- paragraph ordering and transitions
- results anchoring against tables/figures
- section-to-section coherence passes

## Analytical Depth Contract

These depth rules apply across empirical, qualitative, mixed-methods, theory, and methods papers:

- Every substantive paragraph must advance at least two of:
  - mechanism or process
  - tension, comparison, or contradiction
  - alternative explanation
  - boundary condition
  - implication
- Qualitative writing must interpret themes into analytic claims about mechanism, meaning, or scope. Do not stop at theme labels or illustrative quotes.
- If the evidence cannot support a deeper inference, narrow the claim instead of simulating depth with abstract wording.

## Inputs (Ask / Collect)

1. Paper type: **empirical** / **qualitative** / **systematic review** / **theory** / **methods** (default: empirical)
2. Target venue (optional): scope + formatting + double-blind requirements
3. Current artifacts available in `RESEARCH/[topic]/`
4. Citation style (APA/IEEE/BibTeX) and reference source (`bibliography.bib` preferred)

## Inputs

- `RQSet`: Research questions
- `EvidenceTable`: Synthesized evidence
- `DesignSpec`: Study design (for empirical or qualitative papers)
- If a required input is missing or insufficient, write a gap note under `RESEARCH/[topic]/context/gap_notes.md` and ask for the missing artifact instead of inventing content.
- Treat literature, data, citations, and project files as evidence sources; keep unsupported assumptions visibly marked.

## Process

### Step 0: Set Manuscript Folder

Create/ensure:
```
RESEARCH/[topic]/manuscript/
├── outline.md
├── manuscript.md
├── claims_evidence_map.md
└── figures_tables_plan.md
```

### Step 1: Define Contribution & Story Spine

Before writing a word, articulate:

| Element | What to Write | Purpose |
|---------|--------------|---------|
| **Core contribution** | 1–2 sentence "elevator pitch" | Forces clarity of what's new |
| **Novelty points** | 3–5 bullets: what the paper adds that didn't exist before | Feeds Introduction and Discussion |
| **Main thesis** | What the reader should believe after reading | Ensures argumentative coherence |
| **Why the gap persisted** | Why this contribution wasn't made earlier | Elevates above "nobody has studied X" |

**Story spine template**:
```
"Despite [existing knowledge], we still don't understand [gap] because [why gap persisted].
This paper addresses this by [approach], finding that [key results].
This contributes to [theory/field] by [specific theoretical contribution],
and has practical implications for [audience] because [why it matters]."
```

### Step 2: Build Outline with Word Budget

Allocate word budget proportionally:

| Section | Typical % of Total | For 8,000 words | For 12,000 words | Key Function |
|---------|-------------------|-----------------|------------------|-------------|
| Introduction | 10–15% | 800–1,200 | 1,200–1,800 | Establish gap → state contribution |
| Literature / Related Work | 15–20% | 1,200–1,600 | 1,800–2,400 | Position contribution; build theoretical foundation |
| Methods | 15–25% | 1,200–2,000 | 1,800–3,000 | Convince reader the evidence is credible |
| Results / Findings | 20–30% | 1,600–2,400 | 2,400–3,600 | Present evidence systematically |
| Discussion | 15–20% | 1,200–1,600 | 1,800–2,400 | Interpret → contribute to theory → implications |
| Limitations | 3–5% | 240–400 | 360–600 | Honest assessment of scope |
| Conclusion | 3–5% | 240–400 | 360–600 | Summarize contribution; forward-looking |

> **Venue calibration**: Check 3 recent papers in the target venue to verify proportional expectations. Theory journals have longer lit reviews; empirical journals have longer methods/results.

### Step 3: Draft Sections Iteratively

Draft in this order (not the publication order):

#### 3a: Introduction — The Opening Argument

| Paragraph | Job | Template |
|-----------|-----|----------|
| ¶1 | Hook / establish importance | "[Topic] is [significance statement]. [Evidence of importance]." |
| ¶2 | Existing knowledge | "Prior research has established [what we know], including [key findings]." |
| ¶3 | Gap statement | "However, [gap — what remains unknown/unresolved]. This gap persists because [reason]." |
| ¶4 | What this paper does | "This paper addresses this gap by [approach]. Specifically, we [brief design overview]." |
| ¶5 | Preview of contribution + roadmap | "Our findings contribute to [theory] by [contribution]. The paper proceeds as follows: [roadmap]." |

> **Anti-pattern**: "There is a gap in the literature on X" without explaining why the gap matters or persisted. Reviewers want to know why this gap should be filled.

#### 3b: Literature / Related Work

Do NOT write a serial summary of papers. Instead, organize by:

| Organization Style | When to Use | Structure |
|-------------------|------------|-----------|
| **Theme-based** | Established field with clear streams | § per literature stream; end each § positioning your work |
| **Tension-based** | Competing explanations exist | § per debate/tension; position your theory against both sides |
| **Mechanism-based** | Paper proposes a mechanism | § per mechanism candidate; show why yours is needed |
| **Process-based** | Qualitative / temporal phenomenon | § per phase or stage; show what's known about each |

Each literature subsection must end with a "gap statement" that connects to your contribution. Use the literature map from `literature-mapper` (B6) as the skeleton.

> **Anti-pattern**: "Smith (2020) found X. Jones (2021) found Y. Lee (2022) found Z." → This is a list, not a review. Synthesize across papers.

#### 3c: Methods — The Credibility Case

| Subsection | Must Include | Common Failures |
|-----------|-------------|-----------------|
| **Design overview** | Design type + rationale (link to `study-designer` C1) | Design mentioned but not justified |
| **Setting / context** | Where, when, why this setting | Context omitted (reviewer can't assess fit) |
| **Sample / participants** | N, characteristics, recruitment, inclusion/exclusion | No sample size rationale |
| **Data collection** | Instruments, procedures, timing | Interview guide not in supplement |
| **Measures / coding** | Variable definitions, reliability, validation | Measures described but validity not discussed |
| **Analysis procedure** | Estimator, assumptions, steps | "We used regression" without specification |
| **Ethical considerations** | IRB, consent, de-identification | Often forgotten |

#### 3d: Results / Findings — The Evidence Presentation

**For quantitative papers**:

| Component | What to Include |
|-----------|----------------|
| Descriptive statistics | Sample table; correlations |
| Assumption checks | Normality, multicollinearity, outliers |
| Primary analysis | Main model(s) with estimates, CI, p-values |
| Secondary analysis | Subgroups, interactions, mediation |
| Robustness checks | Alternative specifications (main text or appendix) |
| Null results | Report with precision framing — don't bury |

**For qualitative papers**:

| Component | What to Include |
|-----------|----------------|
| Theme overview table | Theme, definition, prevalence, exemplar |
| Theme presentation | Analytical narrative + evidence (quotes, episodes) per theme |
| Cross-case patterns | How themes manifest across cases |
| Deviant / negative cases | Cases that contradict dominant patterns |
| Process model (if applicable) | Visual representation of how themes relate |

> Use `analysis-interpreter` for depth guidance. Every finding should reach Level 2+ on the interpretive depth ladder.

#### 3e: Discussion — The Intellectual Contribution

| Subsection | Job | Common Failure |
|-----------|-----|----------------|
| **Summary of findings** | 1–2 paragraphs recapping key results | Becomes a full results re-presentation |
| **Theoretical contribution** | What does this change or extend in theory? | "Our results are consistent with theory" (so what?) |
| **Comparison to prior work** | Where you agree/disagree with prior findings | Agreement stated without analysis of WHY |
| **Mechanism discussion** | What explains the pattern? | Mechanism asserted without evidence |
| **Boundary conditions** | When does this NOT hold? | Omitted entirely |
| **Practical implications** | What should practitioners do differently? | Overclaimed or too vague |
| **Limitations** | Explicit; linked to specific design choices | All in one paragraph; perfunctory |
| **Future directions** | Each flows from a specific limitation | "Future research should study X" without grounding |

> **Anti-pattern**: Discussion = restated Results + "Companies should...". The Discussion must INTERPRET, not just REPORT + ADVISE.

#### 3f: Abstract, Title, Keywords (Last)

Write these LAST — they must reflect the final, not the planned, paper. Use `meta-optimizer` (F6) for optimization.

### Step 4: Claim–Evidence Integrity Pass

For every non-trivial claim in the manuscript:

| Check | What to Verify | Action if Failing |
|-------|---------------|-------------------|
| **Has evidence** | Claim linked to data/citation | Add evidence or hedge/remove claim |
| **Evidence is sufficient** | Not a single anecdote for a general claim | Add cases or narrow scope |
| **Claim matches evidence strength** | Causal language ↔ causal design | Calibrate language to design |
| **RQ-Methods-Results alignment** | Each RQ addressed in methods AND results | Flag any unaddressed RQ |
| **Speculation labeled** | Hunches clearly distinguished from findings | Add "we speculate that..." framing |

Use `templates/claim-evidence-map.md` to produce:

```markdown
| Claim | Evidence Type | Location | Strength | Status |
|-------|--------------|----------|----------|--------|
| "X increases Y" | Regression β = 0.31, p < .001 | Table 2, § 4.1 | Strong | ✅ |
| "This suggests M drives the relationship" | Mediation analysis + informant accounts | § 4.3, Table 4 | Moderate | ✅ |
| "Could apply to healthcare" | Speculation | § 5.4 | Weak | ⚠️ Label as speculation |
```

### Step 5: Figures/Tables Pass

Use `figure-specifier` (F5) and `table-generator` (F5):

| Check | What to Verify |
|-------|---------------|
| Every figure/table is referenced in text | Look for "Figure 1" and "Table 1" references |
| Every figure/table has a purpose | No decorative visualizations |
| Captions are self-explanatory | Reader can understand without body text |
| Numbering is sequential | Table 1, 2, 3... Figure 1, 2, 3... |
| Data in figures is not duplicated in tables | Choose one format per data point |

### Step 6: Compliance / Readiness Pass

Run the right checker:
- Empirical: **reporting-checker** (CONSORT/STROBE/COREQ/etc.)
- Qualitative: **reporting-checker** (SRQR / COREQ / venue-specific transparency)
- Systematic review: **prisma-checker**

## Output Contract

- `ManuscriptOutline`: write `RESEARCH/[topic]/manuscript/outline.md`.
- `Manuscript`: write `RESEARCH/[topic]/manuscript/manuscript.md`.
- `ClaimGraph`: write `RESEARCH/[topic]/manuscript/claims_evidence_map.md`.
- `FiguresTablesPlan`: write `RESEARCH/[topic]/manuscript/figures_tables_plan.md`.
- Separate finding, interpretation, and implication in the final artifact.
- Do not invent citations, data, sample sizes, statistical results, or reviewer comments.
- Apply `references/academic-output-rubric.md` before finalizing scholarly prose or review artifacts.

### Evidence Ledger and Source Integrity

- Update `RESEARCH/[topic]/evidence/claim-evidence-ledger.csv` when producing, revising, or validating central scholarly claims.
- Follow `references/evidence-ledger-contract.md`: supported claims need source pointers; unsupported central claims become `gap_note` rows and `RESEARCH/[topic]/context/gap_notes.md` entries.
- For final writing, proofread, submission, rebuttal, citation, or presentation-facing outputs, apply `references/citation-risk-policy.md` and write or update `RESEARCH/[topic]/proofread/citation-risk-report.md` when citation risk is material.

## Quality Bar

The manuscript is **ready for review** when:

- [ ] Story spine articulated — contribution clear in first 2 pages
- [ ] Literature organized by theme/tension/mechanism, not by author
- [ ] Methods detailed enough for replication (quant) or audit (qual)
- [ ] Every result has: estimate + CI + effect size (quant) or analytical claim + evidence + deviant case (qual)
- [ ] Discussion interprets (doesn't merely restate) and contributes to theory
- [ ] Claim-evidence map shows no unsupported claims
- [ ] Figures and tables are self-explanatory with adequate captions
- [ ] Reporting checklist completed for the study type
- [ ] Abstract accurately reflects final results

## Outputs

- Outline → `RESEARCH/[topic]/manuscript/outline.md`
- Draft manuscript → `RESEARCH/[topic]/manuscript/manuscript.md`
- Claim-evidence map → `RESEARCH/[topic]/manuscript/claims_evidence_map.md`
- Figures/tables plan → `RESEARCH/[topic]/manuscript/figures_tables_plan.md`

## Notes

- For citation formatting, pair with **citation-formatter**.
- For figure/table design, pair with **figure-specifier** and **table-generator**.
- For final compliance, pair with **reporting-checker** or **prisma-checker**.

## Common Pitfalls

| Pitfall | Problem | Fix |
|---------|---------|-----|
| 结构先行内容后行 | 套模板但论证空洞 | 先建 claim-evidence map 再搭骨架 |
| Introduction 过长 | 读者失去耐心 | 控制在 4-5 段，渐进缩窄 |
| Results 与 Discussion 混合 | 描述与解释交织 | 严格分离（除非期刊要求合并） |
| 图表堆砌 | 太多表格淹没重点 | 核心数据进正文，其余转 appendix |
| Story spine 缺失 | 各章节割裂 | 用一句话总结每节的叙事推进  |

## Political Economy Overlay

### Activation
Apply this overlay when `manuscript-architect` is used for political economy manuscripts connecting political actors, institutions, incentives, distributional conflict, policy processes, and economic outcomes.

### Required Context
- Require the actor set, institution, incentive structure, distributional conflict, policy or economic outcome, method, and target venue family.
- Require the political mechanism before drafting the introduction or theory section.
- Require whether the claim is descriptive, causal, mechanism-based, comparative institutional, or theory-building.

### Subject-Specific Procedure
1. Architect the introduction around the political economy debate and the actor-institution-outcome mechanism.
2. Define actors, incentives, institutional constraints, winners, losers, and policy or economic outcome before presenting evidence.
3. Separate political mechanism evidence from correlations between political variables and outcomes.
4. Connect each central claim to mechanism evidence, rival political or economic mechanisms, and claim strength.
5. Calibrate policy implications when institutional assignment, actor incentives, or timing are not fully identified.

### Reviewer-Risk Checks
- Check whether the manuscript is generic economics without politics or generic political science without a disciplined economic outcome.
- Check whether distributional conflict is implied without naming winners, losers, and incentives.
- Check whether institutional description is decorative rather than part of the mechanism.

### Output Requirements
- The manuscript architecture must include `Actor-Institution-Outcome Map`, `Political Mechanism`, `Rival Mechanisms`, and `Claim Calibration`.
- Each central claim must identify actors, incentives, institution, conflict, outcome, evidence, and gap.
- Missing mechanism evidence must become a revision task or narrowed claim.

### Blocked Conditions
- Block strong causal or policy claims when the political mechanism is not directly evidenced.
- Block final architecture when actors, institutions, incentives, or distributional conflict are absent.
- Do not treat a policy outcome as proof of a political cause.
