dsh-aris-panel 0.1.0

package/skills/skills-codex-gemini-review/paper-write/SKILL.md

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+---
+name: "paper-write"
+description: "Draft LaTeX paper section by section from an outline. Use when user says \"写论文\", \"write paper\", \"draft LaTeX\", \"开始写\", or wants to generate LaTeX content from a paper plan."
+---
+
+> Override for Codex users who want **Gemini**, not a second Codex agent, to act as the reviewer. Install this package **after** `skills/skills-codex/*`.
+
+# Paper Write: Section-by-Section LaTeX Generation
+
+> **Gemini overlay assurance:** `review_independence: cross-family` and `acceptance_status: accepted`.
+
+Draft a LaTeX paper based on: **$ARGUMENTS**
+
+## Constants
+
+- **REVIEWER_MODEL = `gemini-review`** — Gemini reviewer invoked through the local `gemini-review` MCP bridge. Set `GEMINI_REVIEW_MODEL` if you need a specific Gemini model override.
+- **TARGET_VENUE = `ICLR`** — Default venue. Supported: `ICLR`, `NeurIPS`, `ICML`. Determines style file and formatting.
+- **ANONYMOUS = true** — If true, use anonymous author block. Set `false` for camera-ready.
+- **MAX_PAGES = 9** — Main body page limit. Counts from first page to end of Conclusion section. References and appendix are NOT counted.
+- **DBLP_BIBTEX = true** — Fetch real BibTeX from DBLP/CrossRef instead of LLM-generated entries. Eliminates hallucinated citations. Zero install required. Set `false` to use legacy behavior (LLM search + `[VERIFY]` markers).
+
+## Inputs
+
+1. **PAPER_PLAN.md** — outline with claims-evidence matrix, section plan, figure plan (from `/paper-plan`)
+2. **NARRATIVE_REPORT.md** — the research narrative (primary source of content)
+3. **Generated figures** — PDF/PNG files in `figures/` (from `/paper-figure`)
+4. **LaTeX includes** — `figures/latex_includes.tex` (from `/paper-figure`)
+5. **Bibliography** — existing `.bib` file, or will create one
+
+If no PAPER_PLAN.md exists, ask the user to run `/paper-plan` first or provide a brief outline.
+
+## Templates
+
+### Venue-Specific Setup
+
+The skill includes conference templates in `templates/`. Select based on TARGET_VENUE:
+
+**ICLR:**
+```latex
+\documentclass{article}
+\usepackage{iclr2026_conference,times}
+% \iclrfinalcopy  % Uncomment for camera-ready
+```
+
+**NeurIPS:**
+```latex
+\documentclass{article}
+\usepackage[preprint]{neurips_2025}
+% \usepackage[final]{neurips_2025}  % Camera-ready
+```
+
+**ICML:**
+```latex
+\documentclass[accepted]{icml2025}
+% Use [accepted] for camera-ready
+```
+
+### Project Structure
+
+Generate this file structure:
+
+```
+paper/
+├── main.tex                    # master file (includes sections)
+├── iclr2026_conference.sty     # or neurips_2025.sty / icml2025.sty
+├── math_commands.tex           # shared math macros
+├── references.bib              # bibliography (filtered — only cited entries)
+├── sections/
+│   ├── 0_abstract.tex
+│   ├── 1_introduction.tex
+│   ├── 2_related_work.tex
+│   ├── 3_method.tex            # or preliminaries, setup, etc.
+│   ├── 4_experiments.tex
+│   ├── 5_conclusion.tex
+│   └── A_appendix.tex          # proof details, extra experiments
+└── figures/                    # symlink or copy from project figures/
+```
+
+**Section files are FLEXIBLE**: If the paper plan has 6-8 sections, create corresponding files (e.g., `4_theory.tex`, `5_experiments.tex`, `6_analysis.tex`, `7_conclusion.tex`).
+
+## Workflow
+
+### Step 0: Backup and Clean
+
+If `paper/` already exists, back up to `paper-backup-{timestamp}/` before overwriting. Never silently destroy existing work.
+
+**CRITICAL: Clean stale files.** When changing section structure (e.g., 5 sections → 7 sections), delete section files that are no longer referenced by `main.tex`. Stale files (e.g., old `5_conclusion.tex` left behind when conclusion moved to `7_conclusion.tex`) cause confusion and waste space.
+
+### Step 1: Initialize Project
+
+1. Create `paper/` directory
+2. Copy venue template from `templates/` — the template already includes:
+   - All standard packages (amsmath, hyperref, cleveref, booktabs, etc.)
+   - Theorem environments with `\crefname{assumption}` fix
+   - Anonymous author block
+3. Generate `math_commands.tex` with paper-specific notation
+4. Create section files matching PAPER_PLAN structure
+
+**Author block (anonymous mode):**
+```latex
+\author{Anonymous Authors}
+```
+
+### Step 2: Generate math_commands.tex
+
+Create shared math macros based on the paper's notation:
+
+```latex
+% math_commands.tex — shared notation
+\newcommand{\R}{\mathbb{R}}
+\newcommand{\E}{\mathbb{E}}
+\DeclareMathOperator*{\argmin}{arg\,min}
+\DeclareMathOperator*{\argmax}{arg\,max}
+% Add paper-specific notation here
+```
+
+### Step 3: Write Each Section
+
+Process sections in order. For each section:
+
+1. **Read the plan** — what claims, evidence, citations belong here
+2. **Read NARRATIVE_REPORT.md** — extract relevant content, findings, and quantitative results
+3. **Draft content** — write complete LaTeX (not placeholders)
+4. **Insert figures/tables** — use snippets from `figures/latex_includes.tex`
+5. **Add citations** — use `\citep{}` / `\citet{}` (all three venues use `natbib`)
+
+#### Section-Specific Guidelines
+
+**§0 Abstract:**
+- Must be self-contained (understandable without reading the paper)
+- Structure: problem → approach → key result → implication
+- Include one concrete quantitative result
+- 150-250 words (check venue limit)
+- No citations, no undefined acronyms
+- No `\begin{abstract}` — that's in main.tex
+
+**§1 Introduction:**
+- Open with a compelling hook (1-2 sentences, problem motivation)
+- State the gap clearly ("However, ...")
+- List contributions as a numbered or bulleted list
+- End with a brief roadmap ("The rest of this paper is organized as...")
+- Include the main result figure if space allows
+- Target: 1.5 pages
+
+**§2 Related Work:**
+- **MINIMUM 1 full page** (3-4 substantive paragraphs). Short related work sections are a common reviewer complaint.
+- Organize by category using `\paragraph{Category Name.}`
+- Each category: 1 paragraph summarizing the line of work + 1-2 sentences positioning this paper
+- Do NOT just list papers — synthesize and compare
+- End each paragraph with how this paper relates/differs
+
+**§3 Method / Preliminaries / Setup:**
+- Define notation early (reference math_commands.tex)
+- Use `\begin{definition}`, `\begin{theorem}` environments for formal statements
+- For theory papers: include proof sketches of key results in main body, full proofs in appendix
+- For theory papers: include a **comparison table** of prior bounds vs. this paper
+- Include algorithm pseudocode if applicable (`algorithm2e` or `algorithmic`)
+- Target: 1.5-2 pages
+
+**§4 Experiments:**
+- Start with experimental setup (datasets, baselines, metrics, implementation details)
+- Main results table/figure first
+- Then ablations and analysis
+- Every claim from the introduction must have supporting evidence here
+- Target: 2.5-3 pages
+
+**§5 Conclusion:**
+- Summarize contributions (NOT copy-paste from intro — rephrase)
+- Limitations (be honest — reviewers appreciate this)
+- Future work (1-2 concrete directions)
+- Ethics statement and reproducibility statement (if venue requires)
+- Target: 0.5 pages
+
+**Appendix:**
+- Proof details (full proofs of main-body theorems)
+- Additional experiments, ablations
+- Implementation details, hyperparameter tables
+- Additional visualizations
+
+### Step 4: Build Bibliography
+
+**CRITICAL: Only include entries that are actually cited in the paper.**
+
+1. Scan all `\citep{}` and `\citet{}` references in the drafted sections
+2. Build a citation key list
+3. For each citation key:
+   - Check existing `.bib` files in the project/narrative docs
+   - If not found and **DBLP_BIBTEX = true**, use the verified fetch chain below
+   - If not found and **DBLP_BIBTEX = false**, search arXiv/Scholar for correct BibTeX
+   - **NEVER fabricate BibTeX entries** — mark unknown ones with `[VERIFY]` comment
+4. Write `references.bib` containing ONLY cited entries (no bloat)
+
+#### Verified BibTeX Fetch (when DBLP_BIBTEX = true)
+
+Three-step fallback chain — zero install, zero auth, all real BibTeX:
+
+**Step A: DBLP (best quality — full venue, pages, editors)**
+```bash
+# 1. Search by title + first author
+curl -s "https://dblp.org/search/publ/api?q=TITLE+AUTHOR&format=json&h=3"
+# 2. Extract DBLP key from result (e.g., conf/nips/VaswaniSPUJGKP17)
+# 3. Fetch real BibTeX
+curl -s "https://dblp.org/rec/{key}.bib"
+```
+
+**Step B: CrossRef DOI (fallback — works for arXiv preprints)**
+```bash
+# If paper has a DOI or arXiv ID (arXiv DOI = 10.48550/arXiv.{id})
+curl -sLH "Accept: application/x-bibtex" "https://doi.org/{doi}"
+```
+
+**Step C: Mark `[VERIFY]` (last resort)**
+If both DBLP and CrossRef return nothing, mark the entry with `% [VERIFY]` comment. Do NOT fabricate.
+
+**Why this matters:** LLM-generated BibTeX frequently hallucinates venue names, page numbers, or even co-authors. DBLP and CrossRef return publisher-verified metadata. Upstream skills (`/research-lit`, `/novelty-check`) may mention papers from LLM memory — this fetch chain is the gate that prevents hallucinated citations from entering the final `.bib`.
+
+**Automated bib cleaning** — use this Python pattern to extract only cited entries:
+
+```python
+import re
+# 1. Grep all \citep{...} and \citet{...} from all .tex files
+# 2. Extract unique keys (handle multi-cite like \citep{a,b,c})
+# 3. Parse the full .bib file, keep only entries whose key is in the cited set
+# 4. Write the filtered bib
+```
+
+This prevents bib bloat (e.g., 948 lines → 215 lines in testing).
+
+**Citation verification rules (from claude-scholar + Imbad0202):**
+1. Every BibTeX entry must have: author, title, year, venue/journal
+2. Prefer published venue versions over arXiv preprints (if published)
+3. Use consistent key format: `{firstauthor}{year}{keyword}` (e.g., `ho2020denoising`)
+4. Double-check year and venue for every entry
+5. Remove duplicate entries (same paper with different keys)
+
+### Step 5: De-AI Polish (from kgraph57/paper-writer-skill)
+
+After drafting all sections, scan for common AI writing patterns and fix them:
+
+**Content patterns to fix:**
+- Significance inflation ("groundbreaking", "revolutionary" → use measured language)
+- Formulaic transitions ("In this section, we..." → remove or vary)
+- Generic conclusions ("This work opens exciting new avenues" → be specific)
+
+**Language patterns to fix (watch words):**
+- Replace: delve, pivotal, landscape, tapestry, underscore, noteworthy, intriguingly
+- Remove filler: "It is worth noting that", "Importantly,", "Notably,"
+- Avoid rule-of-three lists ("X, Y, and Z" appearing repeatedly)
+- Don't start consecutive sentences with "This" or "We"
+
+### Step 6: Cross-Review with REVIEWER_MODEL
+
+Send the complete draft to Gemini review:
+
+```
+mcp__gemini-review__review_start:
+  prompt: |
+    Review this [VENUE] paper draft (main body, excluding appendix).
+
+    Focus on:
+    1. Does each claim from the intro have supporting evidence?
+    2. Is the writing clear, concise, and free of AI-isms?
+    3. Any logical gaps or unclear explanations?
+    4. Does it fit within [MAX_PAGES] pages (to end of Conclusion)?
+    5. Is related work sufficiently comprehensive (≥1 page)?
+    6. For theory papers: are proof sketches adequate?
+    7. Are figures/tables clearly described and properly referenced?
+
+    For each issue, specify: severity (CRITICAL/MAJOR/MINOR), location, and fix.
+
+    [paste full draft text]
+```
+
+After this start call, immediately save the returned `jobId` and poll `mcp__gemini-review__review_status` with a bounded `waitSeconds` until `done=true`. Treat the completed status payload's `response` as the reviewer output, and save the completed `threadId` for any follow-up round.
+
+Apply CRITICAL and MAJOR fixes. Document MINOR issues for the user.
+
+### Step 7: Reverse Outline Test (from Research-Paper-Writing-Skills)
+
+After drafting all sections:
+
+1. **Extract topic sentences** — pull the first sentence of every paragraph
+2. **Read them in sequence** — they should form a coherent narrative on their own
+3. **Check claim coverage** — every claim from the Claims-Evidence Matrix must appear
+4. **Check evidence mapping** — every experiment/figure must support a stated claim
+5. **Fix gaps** — if a topic sentence doesn't advance the story, rewrite the paragraph
+
+### Step 8: Final Checks
+
+Before declaring done:
+
+- [ ] All `\ref{}` and `\label{}` match (no undefined references)
+- [ ] All `\citep{}` / `\citet{}` have corresponding BibTeX entries
+- [ ] No author information in anonymous mode
+- [ ] Figure/table numbering is correct
+- [ ] Page count within MAX_PAGES (main body to Conclusion end)
+- [ ] No TODO/FIXME/XXX markers left in the text
+- [ ] No `[VERIFY]` markers left unchecked
+- [ ] Abstract is self-contained (understandable without reading the paper)
+- [ ] Title is specific and informative (not generic)
+- [ ] Related work is ≥1 full page
+- [ ] references.bib contains ONLY cited entries (no bloat)
+- [ ] **No stale section files** — every .tex in `sections/` is `\input`ed by `main.tex`
+- [ ] **Section files match main.tex** — file numbering and `\input` paths are consistent
+
+## Output Protocols
+
+> Follow these shared protocols for all output files:
+> - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
+> - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
+> - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting
+
+## Key Rules
+
+- **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
+
+- **Do NOT generate author names, emails, or affiliations** — use anonymous block or placeholder
+- **Write complete sections, not outlines** — the output should be compilable LaTeX
+- **One file per section** — modular structure for easy editing
+- **Every claim must cite evidence** — cross-reference the Claims-Evidence Matrix
+- **Compile-ready** — the output should compile with `latexmk` without errors (modulo missing figures)
+- **No over-claiming** — use hedging language ("suggests", "indicates") for weak evidence
+- **Venue style matters** — all three venues (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`)
+- **Page limit = main body to Conclusion** — references and appendix do NOT count
+- **Clean bib** — references.bib must only contain entries that are actually `\cite`d
+- **Section count is flexible** — match PAPER_PLAN structure, don't force into 5 sections
+- **Backup before overwrite** — never destroy existing `paper/` directory without backing up
+
+## Writing Quality Reference
+
+Principles from [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills):
+
+1. **One message per paragraph** — each paragraph makes exactly one point
+2. **Topic sentence first** — the first sentence states the paragraph's message
+3. **Explicit transitions** — connect paragraphs with logical connectors
+4. **Reverse outline test** — extract topic sentences; they should form a coherent narrative
+
+De-AI patterns from [kgraph57/paper-writer-skill](https://github.com/kgraph57/paper-writer-skill):
+
+5. **No AI watch words** — delve, pivotal, landscape, tapestry, underscore
+6. **No significance inflation** — groundbreaking, revolutionary, paradigm shift
+7. **No formulaic structures** — vary sentence openings and transitions
+
+## Acknowledgements
+
+Writing methodology adapted from [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills) (CCF award-winning methodology). Citation verification from [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills). De-AI polish from [kgraph57/paper-writer-skill](https://github.com/kgraph57/paper-writer-skill). Backup mechanism from [baoyu-skills](https://github.com/jimliu/baoyu-skills).

package/skills/skills-codex-gemini-review/paper-writing/SKILL.md

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+---
+name: "paper-writing"
+description: "Workflow 3: Full paper writing pipeline. Orchestrates paper-plan \u2192 paper-figure \u2192 paper-write \u2192 paper-compile \u2192 auto-paper-improvement-loop to go from a narrative report to a polished, submission-ready PDF. Use when user says \\\"\u5199\u8bba\u6587\u5168\u6d41\u7a0b\\\", \\\"write paper pipeline\\\", \\\"\u4ece\u62a5\u544a\u5230PDF\\\", \\\"paper writing\\\", or wants the complete paper generation workflow."
+---
+
+> Override for Codex users who want **Gemini**, not a second Codex agent, to act as the reviewer. Install this package **after** `skills/skills-codex/*`.
+
+# Workflow 3: Paper Writing Pipeline
+
+> **Gemini overlay assurance:** `review_independence: cross-family` and `acceptance_status: accepted`.
+
+Orchestrate a complete paper writing workflow for: **$ARGUMENTS**
+
+## Overview
+
+This skill chains five sub-skills into a single automated pipeline:
+
+```
+/paper-plan → /paper-figure → /paper-write → /paper-compile → /auto-paper-improvement-loop
+  (outline)     (plots)        (LaTeX)        (build PDF)       (review & polish ×2)
+```
+
+Each phase builds on the previous one's output. The final deliverable is a polished, reviewed `paper/` directory with LaTeX source and compiled PDF.
+
+## Constants
+
+- **VENUE = `ICLR`** — Target venue. Options: `ICLR`, `NeurIPS`, `ICML`. Affects style file, page limit, citation format.
+- **MAX_IMPROVEMENT_ROUNDS = 2** — Number of review→fix→recompile rounds in the improvement loop.
+- **REVIEWER_MODEL = `gemini-review`** — Gemini reviewer invoked through the local `gemini-review` MCP bridge for plan review, figure review, writing review, and the improvement loop.
+- **AUTO_PROCEED = true** — Auto-continue between phases. Set `false` to pause and wait for user approval after each phase.
+- **HUMAN_CHECKPOINT = false** — When `true`, the improvement loop (Phase 5) pauses after each round's review to let you see the score and provide custom modification instructions. When `false` (default), the loop runs fully autonomously. Passed through to `/auto-paper-improvement-loop`.
+
+> Override inline: `/paper-writing "NARRATIVE_REPORT.md" — venue: NeurIPS, human checkpoint: true`
+
+## Inputs
+
+This pipeline accepts one of:
+
+1. **`NARRATIVE_REPORT.md`** (best) — structured research narrative with claims, experiments, results, figures
+2. **Research direction + experiment results** — the skill will help draft the narrative first
+3. **Existing `PAPER_PLAN.md`** — skip Phase 1, start from Phase 2
+
+The more detailed the input (especially figure descriptions and quantitative results), the better the output.
+
+## Pipeline
+
+### Phase 1: Paper Plan
+
+Invoke `/paper-plan` to create the structural outline:
+
+```
+/paper-plan "$ARGUMENTS"
+```
+
+**What this does:**
+- Parse NARRATIVE_REPORT.md for claims, evidence, and figure descriptions
+- Build a **Claims-Evidence Matrix** — every claim maps to evidence, every experiment supports a claim
+- Design section structure (5-8 sections depending on paper type)
+- Plan figure/table placement with data sources
+- Scaffold citation structure
+- Gemini reviews the plan for completeness via the `/paper-plan` overlay
+
+**Output:** `PAPER_PLAN.md` with section plan, figure plan, citation scaffolding.
+
+**Checkpoint:** Present the plan summary to the user.
+
+```
+📐 Paper plan complete:
+- Title: [proposed title]
+- Sections: [N] ([list])
+- Figures: [N] auto-generated + [M] manual
+- Target: [VENUE], [PAGE_LIMIT] pages
+
+Shall I proceed with figure generation?
+```
+
+- **User approves** (or AUTO_PROCEED=true) → proceed to Phase 2.
+- **User requests changes** → adjust plan and re-present.
+
+### Phase 2: Figure Generation
+
+Invoke `/paper-figure` to generate data-driven plots and tables:
+
+```
+/paper-figure "PAPER_PLAN.md"
+```
+
+**What this does:**
+- Read figure plan from PAPER_PLAN.md
+- Generate matplotlib/seaborn plots from JSON/CSV data
+- Generate LaTeX comparison tables
+- Create `figures/latex_includes.tex` for easy insertion
+- Gemini reviews figure quality and captions via the `/paper-figure` overlay
+
+**Output:** `figures/` directory with PDFs, generation scripts, and LaTeX snippets.
+
+#### Phase 2b: AI Illustration Generation (when `illustration: true`)
+
+**Skip this step entirely if `illustration` is not set or is `false`.**
+
+If the paper plan includes architecture diagrams, pipeline figures, or method illustrations, invoke `/paper-illustration`:
+
+```
+/paper-illustration "[method description from PAPER_PLAN.md or NARRATIVE_REPORT.md]"
+```
+
+**What this does:**
+- Codex plans the layout → Gemini optimizes → Nano Banana Pro renders → Codex reviews (score ≥ 9)
+- Output: `figures/ai_generated/*.png` — publication-quality method diagrams
+- Requires `GEMINI_API_KEY` environment variable
+
+> **Without `illustration: true`:** Architecture diagrams must still be created manually (draw.io, Figma, TikZ) and placed in `figures/` before proceeding — same as before.
+
+**Checkpoint:** List generated vs manual figures.
+
+```
+📊 Figures complete:
+- Data plots (auto): [list]
+- AI illustrations (auto): [list, if illustration: true]
+- Manual (need your input): [list]
+- LaTeX snippets: figures/latex_includes.tex
+
+[If manual figures needed]: Please add them to figures/ before I proceed.
+[If all auto]: Shall I proceed with LaTeX writing?
+```
+
+### Phase 3: LaTeX Writing
+
+Invoke `/paper-write` to generate section-by-section LaTeX:
+
+```
+/paper-write "PAPER_PLAN.md"
+```
+
+**What this does:**
+- Write each section following the plan, with proper LaTeX formatting
+- Insert figure/table references from `figures/latex_includes.tex`
+- Build `references.bib` from citation scaffolding
+- Clean stale files from previous section structures
+- Automated bib cleaning (remove uncited entries)
+- De-AI polish (remove "delve", "pivotal", "landscape"...)
+- Gemini reviews each section for quality via the `/paper-write` overlay
+
+**Output:** `paper/` directory with `main.tex`, `sections/*.tex`, `references.bib`, `math_commands.tex`.
+
+**Checkpoint:** Report section completion.
+
+```
+✍️ LaTeX writing complete:
+- Sections: [N] written ([list])
+- Citations: [N] unique keys in references.bib
+- Stale files cleaned: [list, if any]
+
+Shall I proceed with compilation?
+```
+
+### Phase 4: Compilation
+
+Invoke `/paper-compile` to build the PDF:
+
+```
+/paper-compile "paper/"
+```
+
+**What this does:**
+- `latexmk -pdf` with automatic multi-pass compilation
+- Auto-fix common errors (missing packages, undefined refs, BibTeX syntax)
+- Up to 3 compilation attempts
+- Post-compilation checks: undefined refs, page count, font embedding
+- Precise page verification via `pdftotext`
+- Stale file detection
+
+**Output:** `paper/main.pdf`
+
+**Checkpoint:** Report compilation results.
+
+```
+🔨 Compilation complete:
+- Status: SUCCESS
+- Pages: [X] (main body) + [Y] (references) + [Z] (appendix)
+- Within page limit: YES/NO
+- Undefined references: 0
+- Undefined citations: 0
+
+Shall I proceed with the improvement loop?
+```
+
+### Phase 5: Auto Improvement Loop
+
+Invoke `/auto-paper-improvement-loop` to polish the paper:
+
+```
+/auto-paper-improvement-loop "paper/"
+```
+
+**What this does (2 rounds):**
+
+**Round 1:** Gemini reviews the full paper → identifies CRITICAL/MAJOR/MINOR issues → Codex implements fixes → recompile → save `main_round1.pdf`
+
+**Round 2:** Gemini re-reviews with conversation context → identifies remaining issues → Codex implements fixes → recompile → save `main_round2.pdf`
+
+**Typical improvements:**
+- Fix assumption-model mismatches
+- Soften overclaims to match evidence
+- Add missing interpretations and notation
+- Strengthen limitations section
+- Add theory-aligned experiments if needed
+
+**Output:** Three PDFs for comparison + `PAPER_IMPROVEMENT_LOG.md`.
+
+**Format check** (included in improvement loop Step 8): After final recompilation, auto-detect and fix overfull hboxes (content exceeding margins), verify page count vs venue limit, and ensure compact formatting. Any overfull > 10pt is fixed before generating the final PDF.
+
+### Phase 5.9: Integrity Forensics (opt-in — Codex executor rules apply)
+
+Same contract as the base Codex pack (`skills-codex/paper-writing` Phase 5.9,
+which this overlay does not change): the executor here is Codex, so only
+upstream's **deterministic-only slice** of `/integrity-forensics` is runnable
+(numeric core + rules-only reporter — it can flag, it can never say
+CLEAN), OFF unless the CURRENT `$ARGUMENTS` contains `— self_forensics:
+true`. If opted in: run the launcher on `paper/` (absolute path), then before
+the Final Report require `python3 "$GATE_HELPER" fresh --paper-dir paper/
+--anti-ar-commit "$ANTI_AR_COMMIT"` exit 0 — an opted-in run without a fresh gate is **incomplete, not
+skippable**; gate `BLOCK` refuses the Final Report.
+
+### Phase 6: Final Report
+
+```markdown
+# Paper Writing Pipeline Report
+
+**Input**: [NARRATIVE_REPORT.md or topic]
+**Venue**: [ICLR/NeurIPS/ICML]
+**Forensics**: [NO_NEW_BLOCKER | WARN: <n> open obligations (listed below) | BLOCK | n/a (opt-in, not requested)]
+**Date**: [today]
+
+## Pipeline Summary
+
+| Phase | Status | Output |
+|-------|--------|--------|
+| 1. Paper Plan | ✅ | PAPER_PLAN.md |
+| 2. Figures | ✅ | figures/ ([N] auto + [M] manual) |
+| 3. LaTeX Writing | ✅ | paper/sections/*.tex ([N] sections, [M] citations) |
+| 4. Compilation | ✅ | paper/main.pdf ([X] pages) |
+| 5. Improvement | ✅ | [score0]/10 → [score2]/10 |
+
+## Improvement Scores
+| Round | Score | Key Changes |
+|-------|-------|-------------|
+| Round 0 | X/10 | Baseline |
+| Round 1 | Y/10 | [summary] |
+| Round 2 | Z/10 | [summary] |
+
+## Deliverables
+- paper/main.pdf — Final polished paper
+- paper/main_round0_original.pdf — Before improvement
+- paper/main_round1.pdf — After round 1
+- paper/main_round2.pdf — After round 2
+- paper/PAPER_IMPROVEMENT_LOG.md — Full review log
+
+## Remaining Issues (if any)
+- [items from final review that weren't addressed]
+
+## Next Steps
+- [ ] Visual inspection of PDF
+- [ ] Add any missing manual figures
+- [ ] Submit to [venue] via OpenReview / CMT / HotCRP
+```
+
+## Output Protocols
+
+> Follow these shared protocols for all output files:
+> - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
+> - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
+> - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting
+> - Note: paper content is always written in English regardless of project language setting.
+
+## Key Rules
+
+- **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
+
+- **Don't skip phases.** Each phase builds on the previous one — skipping leads to errors.
+- **Checkpoint between phases** when AUTO_PROCEED=false. Present results and wait for approval.
+- **Manual figures first.** If the paper needs architecture diagrams or qualitative results, the user must provide them before Phase 3.
+- **Compilation must succeed** before entering the improvement loop. Fix all errors first.
+- **Preserve all PDFs.** The user needs round0/round1/round2 for comparison.
+- **Document everything.** The pipeline report should be self-contained.
+- **Respect page limits.** If the paper exceeds the venue limit, suggest specific cuts before the improvement loop.
+
+## Composing with Other Workflows
+
+```
+/idea-discovery "direction"         ← Workflow 1: find ideas
+implement                           ← write code
+/run-experiment                     ← deploy experiments
+/auto-review-loop "paper topic"     ← Workflow 2: iterate research
+/paper-writing "NARRATIVE_REPORT.md"  ← Workflow 3: you are here
+                                         submit! 🎉
+
+Or use /research-pipeline for the Workflow 1+2 end-to-end flow,
+then /paper-writing for the final writing step.
+```
+
+## Typical Timeline
+
+| Phase | Duration | Can sleep? |
+|-------|----------|------------|
+| 1. Paper Plan | 5-10 min | No |
+| 2. Figures | 5-15 min | No |
+| 3. LaTeX Writing | 15-30 min | Yes ✅ |
+| 4. Compilation | 2-5 min | No |
+| 5. Improvement | 15-30 min | Yes ✅ |
+
+**Total: ~45-90 min** for a full paper from narrative report to polished PDF.