@bohuyeshan/openagent-labforge-core 3.11.5 → 3.13.0

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-plan/SKILL.md

@@ -6,249 +6,250 @@ allowed-tools: "Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFet
 metadata:
   category: "research/document-authoring"
 ---
-# Paper Plan: From Review Conclusions to Paper Outline
-
-Generate a structured, section-by-section paper outline from: **$ARGUMENTS**
-
-## Constants
-
-- **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for outline review. Must be an OpenAI model.
-- **TARGET_VENUE = `ICLR`** — Default venue. User can override (e.g., `/paper-plan "topic" — venue: NeurIPS`). Supported: `ICLR`, `NeurIPS`, `ICML`.
-- **MAX_PAGES** — Main body page limit, measured from first page to end of Conclusion section (excluding references, appendix, and acknowledgements). ICLR=9, NeurIPS=9, ICML=8.
-
-## Inputs
-
-The skill expects one or more of these in the project directory:
-
-1. **NARRATIVE_REPORT.md** or **STORY.md** — research narrative with claims and evidence
-2. **Experiment results** — JSON files in `figures/`, screen logs, tables
-3. **IDEA_REPORT.md** — from idea-discovery pipeline (if applicable)
-
-If none exist, ask the user to describe the paper's contribution in 3-5 sentences.
-
-## Workflow
-
-### Step 1: Extract Claims and Evidence
-
-Read all available narrative documents and extract:
-
-1. **Core claims** (3-5 main contributions)
-2. **Evidence** for each claim (which experiments, which metrics, which figures)
-3. **Known weaknesses** (from reviewer feedback)
-4. **Suggested framing** (from review conclusions)
-
-Build a **Claims-Evidence Matrix**:
-
-```markdown
-| Claim | Evidence | Status | Section |
-|-------|----------|--------|---------|
-| [claim 1] | [exp A, metric B] | Supported | §3.2 |
-| [claim 2] | [exp C] | Partially supported | §4.1 |
-```
-
-### Step 2: Determine Paper Type and Structure
-
-Based on TARGET_VENUE and paper content, classify and select structure.
-
-**IMPORTANT**: The section count is FLEXIBLE (5-8 sections). Choose what fits the content best. The templates below are starting points, not rigid constraints.
-
-**Empirical/Diagnostic paper:**
-```
-1. Introduction (1.5 pages)
-2. Related Work (1 page)
-3. Method / Setup (1.5 pages)
-4. Experiments (3 pages)
-5. Analysis / Discussion (1 page)
-6. Conclusion (0.5 pages)
-```
-
-**Theory + Experiments paper:**
-```
-1. Introduction (1.5 pages)
-2. Related Work (1 page)
-3. Preliminaries & Modeling (1.5 pages)
-4. Experiments (1.5 pages)
-5. Theory Part A (1.5 pages)
-6. Theory Part B (1.5 pages)
-7. Conclusion (0.5 pages)
-— Total: 9 pages
-```
-Theory papers often need 7 sections (splitting theory into estimation + optimization, or setup + analysis). The total page budget MUST sum to MAX_PAGES.
-
-Theory papers should:
-- Include **proof sketch** locations (not just theorem statements)
-- Plan a **comparison table** of prior theoretical bounds vs. this paper's bounds
-- Identify which proofs go in appendix vs. main body
-
-**Method paper:**
-```
-1. Introduction (1.5 pages)
-2. Related Work (1 page)
-3. Method (2 pages)
-4. Experiments (2.5 pages)
-5. Ablation / Analysis (1 page)
-6. Conclusion (0.5 pages)
-```
-
-### Step 3: Section-by-Section Planning
-
-For each section, specify:
-
-```markdown
-### §0 Abstract
-- **One-sentence problem**: [what gap this paper addresses]
-- **Approach**: [what we do, in one sentence]
-- **Key result**: [most compelling quantitative finding]
-- **Implication**: [why it matters]
-- **Estimated length**: 150-250 words
-- **Self-contained check**: can a reader understand this without the paper?
-
-### §1 Introduction
-- **Opening hook**: [1-2 sentences that motivate the problem]
-- **Gap**: [what's missing in prior work]
-- **Key questions**: [the research questions this paper answers]
-- **Contributions**: [numbered list, matching Claims-Evidence Matrix]
-- **Hero figure**: [describe what Figure 1 should show — MUST include clear comparison if applicable]
-- **Estimated length**: 1.5 pages
-- **Key citations**: [3-5 papers to cite here]
-
-### §2 Related Work
-- **Subtopics**: [2-4 categories of related work]
-- **Positioning**: [how this paper differs from each category]
-- **Minimum length**: 1 full page (at least 3-4 paragraphs with substantive synthesis)
-- **Must NOT be just a list** — synthesize, compare, and position
-
-### §3 Method / Setup / Preliminaries
-- **Notation**: [key symbols and their meanings]
-- **Problem formulation**: [formal setup]
-- **Method description**: [algorithm, model, or experimental design]
-- **Formal statements**: [theorems, propositions if applicable]
-- **Proof sketch locations**: [which key steps appear here vs. appendix]
-- **Estimated length**: 1.5-2 pages
-
-### §4 Experiments / Main Results
-- **Figures planned**:
-  - Fig 1: [description, type: bar/line/table/architecture, WHAT COMPARISON it shows]
-  - Fig 2: [description]
-  - Table 1: [what it shows, which methods/baselines compared]
-- **Data source**: [which JSON files / experiment results]
-
-### §5 Conclusion
-- **Restatement**: [contributions rephrased, not copy-pasted from intro]
-- **Limitations**: [honest assessment — reviewers value this]
-- **Future work**: [1-2 concrete directions]
-- **Estimated length**: 0.5 pages
-```
-
-### Step 4: Figure Plan
-
-List every figure and table:
-
-```markdown
-## Figure Plan
-
-| ID | Type | Description | Data Source | Priority |
-|----|------|-------------|-------------|----------|
-| Fig 1 | Hero/Architecture | System overview + comparison | manual | HIGH |
-| Fig 2 | Line plot | Training curves comparison | figures/exp_A.json | HIGH |
-| Fig 3 | Bar chart | Ablation results | figures/ablation.json | MEDIUM |
-| Table 1 | Comparison table | Main results vs. baselines | figures/main_results.json | HIGH |
-| Table 2 | Theory comparison | Prior bounds vs. ours | manual | HIGH (theory papers) |
-```
-
-**CRITICAL for Figure 1 / Hero Figure**: Describe in detail what the figure should contain, including:
-- Which methods are being compared
-- What the visual difference should demonstrate
-- Caption draft that clearly states the comparison
-
-### Step 5: Citation Scaffolding
-
-For each section, list required citations:
-
-```markdown
-## Citation Plan
-- §1 Intro: [paper1], [paper2], [paper3] (problem motivation)
-- §2 Related: [paper4]-[paper10] (categorized by subtopic)
-- §3 Method: [paper11] (baseline), [paper12] (technique we build on)
-```
-
-**Citation rules** (from claude-scholar + Imbad0202/academic-research-skills):
-1. NEVER generate BibTeX from memory — always verify via search or existing .bib files
-2. Every citation must be verified: correct authors, year, venue
-3. Flag any citation you're unsure about with `[VERIFY]`
-4. Prefer published versions over arXiv preprints when available
-
-### Step 6: Cross-Review with REVIEWER_MODEL
-
-Send the complete outline to GPT-5.4 xhigh for feedback:
-
-```
-mcp__codex__codex:
-  model: gpt-5.4
-  config: {"model_reasoning_effort": "xhigh"}
-  prompt: |
-    Review this paper outline for a [VENUE] submission.
-    [full outline including Claims-Evidence Matrix]
-
-    Score 1-10 on:
-    1. Logical flow — does the story build naturally?
-    2. Claim-evidence alignment — every claim backed?
-    3. Missing experiments or analysis
-    4. Positioning relative to prior work
-    5. Page budget feasibility (MAX_PAGES = main body to Conclusion end, excluding refs/appendix)
-
-    For each weakness, suggest the MINIMUM fix.
-    Be specific and actionable — "add X" not "consider more experiments".
-```
-
-Apply feedback before finalizing.
-
-### Step 7: Output
-
-Save the final outline to `PAPER_PLAN.md` in the project root:
-
-```markdown
-# Paper Plan
-
-**Title**: [working title]
-**Venue**: [target venue]
-**Type**: [empirical/theory/method]
-**Date**: [today]
-**Page budget**: [MAX_PAGES] pages (main body to Conclusion end, excluding references & appendix)
-**Section count**: [N] (must match the number of section files that will be created)
-
-## Claims-Evidence Matrix
-[from Step 1]
-
-## Structure
-[from Step 2-3, section by section]
-
-## Figure Plan
-[from Step 4, with detailed hero figure description]
-
-## Citation Plan
-[from Step 5]
-
-## Reviewer Feedback
-[from Step 6, summarized]
-
-## Next Steps
-- [ ] /paper-figure to generate all figures
-- [ ] /paper-write to draft LaTeX
-- [ ] /paper-compile to build PDF
-```
-
-## Key Rules
-
-- **Do NOT generate author information** — leave author block as placeholder or anonymous
-- **Be honest about evidence gaps** — mark claims as "needs experiment" rather than overclaiming
-- **Page budget is hard** — if content exceeds MAX_PAGES, suggest what to move to appendix
-- **MAX_PAGES counts main body only** — from first page to end of Conclusion. References and appendix are NOT counted.
-- **Venue-specific norms** — all three venues (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`)
-- **Claims-Evidence Matrix is the backbone** — every claim must map to evidence, every experiment must support a claim
-- **Figures need detailed descriptions** — especially the hero figure, which must clearly specify comparisons and visual expectations
-- **Section count is flexible** — 5-8 sections depending on paper type. Don't force content into a rigid 5-section template.
-
-## Acknowledgements
-
-Outline methodology inspired by [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills) (claim-evidence mapping), [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) (citation verification), and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills) (claim verification protocol).
+
+# Paper Plan: From Review Conclusions to Paper Outline
+
+Generate a structured, section-by-section paper outline from: **$ARGUMENTS**
+
+## Constants
+
+- **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for outline review. Must be an OpenAI model.
+- **TARGET_VENUE = `ICLR`** — Default venue. User can override (e.g., `/paper-plan "topic" — venue: NeurIPS`). Supported: `ICLR`, `NeurIPS`, `ICML`.
+- **MAX_PAGES** — Main body page limit, measured from first page to end of Conclusion section (excluding references, appendix, and acknowledgements). ICLR=9, NeurIPS=9, ICML=8.
+
+## Inputs
+
+The skill expects one or more of these in the project directory:
+
+1. **NARRATIVE_REPORT.md** or **STORY.md** — research narrative with claims and evidence
+2. **Experiment results** — JSON files in `figures/`, screen logs, tables
+3. **IDEA_REPORT.md** — from idea-discovery pipeline (if applicable)
+
+If none exist, ask the user to describe the paper's contribution in 3-5 sentences.
+
+## Workflow
+
+### Step 1: Extract Claims and Evidence
+
+Read all available narrative documents and extract:
+
+1. **Core claims** (3-5 main contributions)
+2. **Evidence** for each claim (which experiments, which metrics, which figures)
+3. **Known weaknesses** (from reviewer feedback)
+4. **Suggested framing** (from review conclusions)
+
+Build a **Claims-Evidence Matrix**:
+
+```markdown
+| Claim | Evidence | Status | Section |
+|-------|----------|--------|---------|
+| [claim 1] | [exp A, metric B] | Supported | §3.2 |
+| [claim 2] | [exp C] | Partially supported | §4.1 |
+```
+
+### Step 2: Determine Paper Type and Structure
+
+Based on TARGET_VENUE and paper content, classify and select structure.
+
+**IMPORTANT**: The section count is FLEXIBLE (5-8 sections). Choose what fits the content best. The templates below are starting points, not rigid constraints.
+
+**Empirical/Diagnostic paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Method / Setup (1.5 pages)
+4. Experiments (3 pages)
+5. Analysis / Discussion (1 page)
+6. Conclusion (0.5 pages)
+```
+
+**Theory + Experiments paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Preliminaries & Modeling (1.5 pages)
+4. Experiments (1.5 pages)
+5. Theory Part A (1.5 pages)
+6. Theory Part B (1.5 pages)
+7. Conclusion (0.5 pages)
+— Total: 9 pages
+```
+Theory papers often need 7 sections (splitting theory into estimation + optimization, or setup + analysis). The total page budget MUST sum to MAX_PAGES.
+
+Theory papers should:
+- Include **proof sketch** locations (not just theorem statements)
+- Plan a **comparison table** of prior theoretical bounds vs. this paper's bounds
+- Identify which proofs go in appendix vs. main body
+
+**Method paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Method (2 pages)
+4. Experiments (2.5 pages)
+5. Ablation / Analysis (1 page)
+6. Conclusion (0.5 pages)
+```
+
+### Step 3: Section-by-Section Planning
+
+For each section, specify:
+
+```markdown
+### §0 Abstract
+- **One-sentence problem**: [what gap this paper addresses]
+- **Approach**: [what we do, in one sentence]
+- **Key result**: [most compelling quantitative finding]
+- **Implication**: [why it matters]
+- **Estimated length**: 150-250 words
+- **Self-contained check**: can a reader understand this without the paper?
+
+### §1 Introduction
+- **Opening hook**: [1-2 sentences that motivate the problem]
+- **Gap**: [what's missing in prior work]
+- **Key questions**: [the research questions this paper answers]
+- **Contributions**: [numbered list, matching Claims-Evidence Matrix]
+- **Hero figure**: [describe what Figure 1 should show — MUST include clear comparison if applicable]
+- **Estimated length**: 1.5 pages
+- **Key citations**: [3-5 papers to cite here]
+
+### §2 Related Work
+- **Subtopics**: [2-4 categories of related work]
+- **Positioning**: [how this paper differs from each category]
+- **Minimum length**: 1 full page (at least 3-4 paragraphs with substantive synthesis)
+- **Must NOT be just a list** — synthesize, compare, and position
+
+### §3 Method / Setup / Preliminaries
+- **Notation**: [key symbols and their meanings]
+- **Problem formulation**: [formal setup]
+- **Method description**: [algorithm, model, or experimental design]
+- **Formal statements**: [theorems, propositions if applicable]
+- **Proof sketch locations**: [which key steps appear here vs. appendix]
+- **Estimated length**: 1.5-2 pages
+
+### §4 Experiments / Main Results
+- **Figures planned**:
+  - Fig 1: [description, type: bar/line/table/architecture, WHAT COMPARISON it shows]
+  - Fig 2: [description]
+  - Table 1: [what it shows, which methods/baselines compared]
+- **Data source**: [which JSON files / experiment results]
+
+### §5 Conclusion
+- **Restatement**: [contributions rephrased, not copy-pasted from intro]
+- **Limitations**: [honest assessment — reviewers value this]
+- **Future work**: [1-2 concrete directions]
+- **Estimated length**: 0.5 pages
+```
+
+### Step 4: Figure Plan
+
+List every figure and table:
+
+```markdown
+## Figure Plan
+
+| ID | Type | Description | Data Source | Priority |
+|----|------|-------------|-------------|----------|
+| Fig 1 | Hero/Architecture | System overview + comparison | manual | HIGH |
+| Fig 2 | Line plot | Training curves comparison | figures/exp_A.json | HIGH |
+| Fig 3 | Bar chart | Ablation results | figures/ablation.json | MEDIUM |
+| Table 1 | Comparison table | Main results vs. baselines | figures/main_results.json | HIGH |
+| Table 2 | Theory comparison | Prior bounds vs. ours | manual | HIGH (theory papers) |
+```
+
+**CRITICAL for Figure 1 / Hero Figure**: Describe in detail what the figure should contain, including:
+- Which methods are being compared
+- What the visual difference should demonstrate
+- Caption draft that clearly states the comparison
+
+### Step 5: Citation Scaffolding
+
+For each section, list required citations:
+
+```markdown
+## Citation Plan
+- §1 Intro: [paper1], [paper2], [paper3] (problem motivation)
+- §2 Related: [paper4]-[paper10] (categorized by subtopic)
+- §3 Method: [paper11] (baseline), [paper12] (technique we build on)
+```
+
+**Citation rules** (from claude-scholar + Imbad0202/academic-research-skills):
+1. NEVER generate BibTeX from memory — always verify via search or existing .bib files
+2. Every citation must be verified: correct authors, year, venue
+3. Flag any citation you're unsure about with `[VERIFY]`
+4. Prefer published versions over arXiv preprints when available
+
+### Step 6: Cross-Review with REVIEWER_MODEL
+
+Send the complete outline to GPT-5.4 xhigh for feedback:
+
+```
+mcp__codex__codex:
+  model: gpt-5.4
+  config: {"model_reasoning_effort": "xhigh"}
+  prompt: |
+    Review this paper outline for a [VENUE] submission.
+    [full outline including Claims-Evidence Matrix]
+
+    Score 1-10 on:
+    1. Logical flow — does the story build naturally?
+    2. Claim-evidence alignment — every claim backed?
+    3. Missing experiments or analysis
+    4. Positioning relative to prior work
+    5. Page budget feasibility (MAX_PAGES = main body to Conclusion end, excluding refs/appendix)
+
+    For each weakness, suggest the MINIMUM fix.
+    Be specific and actionable — "add X" not "consider more experiments".
+```
+
+Apply feedback before finalizing.
+
+### Step 7: Output
+
+Save the final outline to `PAPER_PLAN.md` in the project root:
+
+```markdown
+# Paper Plan
+
+**Title**: [working title]
+**Venue**: [target venue]
+**Type**: [empirical/theory/method]
+**Date**: [today]
+**Page budget**: [MAX_PAGES] pages (main body to Conclusion end, excluding references & appendix)
+**Section count**: [N] (must match the number of section files that will be created)
+
+## Claims-Evidence Matrix
+[from Step 1]
+
+## Structure
+[from Step 2-3, section by section]
+
+## Figure Plan
+[from Step 4, with detailed hero figure description]
+
+## Citation Plan
+[from Step 5]
+
+## Reviewer Feedback
+[from Step 6, summarized]
+
+## Next Steps
+- [ ] /paper-figure to generate all figures
+- [ ] /paper-write to draft LaTeX
+- [ ] /paper-compile to build PDF
+```
+
+## Key Rules
+
+- **Do NOT generate author information** — leave author block as placeholder or anonymous
+- **Be honest about evidence gaps** — mark claims as "needs experiment" rather than overclaiming
+- **Page budget is hard** — if content exceeds MAX_PAGES, suggest what to move to appendix
+- **MAX_PAGES counts main body only** — from first page to end of Conclusion. References and appendix are NOT counted.
+- **Venue-specific norms** — all three venues (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`)
+- **Claims-Evidence Matrix is the backbone** — every claim must map to evidence, every experiment must support a claim
+- **Figures need detailed descriptions** — especially the hero figure, which must clearly specify comparisons and visual expectations
+- **Section count is flexible** — 5-8 sections depending on paper type. Don't force content into a rigid 5-section template.
+
+## Acknowledgements
+
+Outline methodology inspired by [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills) (claim-evidence mapping), [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) (citation verification), and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills) (claim verification protocol).