<required_reading> @~/.maestro/workflows/run-mode.md </required_reading>

Scholar Writing

End-to-end workflow for writing publication-ready ML/AI papers from research repositories. Integrates paper writing craft, citation verification, and anti-AI polishing into a structured 6-phase pipeline.

Run Lifecycle

Follow ~/.maestro/workflows/run-mode.md. If an orchestrator injected run_id / run_dir in the birth packet, use them and do NOT call maestro run create. Otherwise self-start before Phase 1:

bash
maestro run create scholar-writing --session <YYYYMMDD-scholar-writing-{topic}> --intent "<short phrase>"

Session slug is ASCII-only, ≤64 chars. The paper itself lives in the user's outputDir (a working area in the user's repo, like source code — not the Run truth source). Write the workflow synthesis and the delivery manifest (paths to paper.tex / paper.pdf / references.bib, verification status, remaining action items) to {run_dir}/report.md, and the machine-readable delivery-paths list to {run_dir}/outputs/delivery.json — the contract registers it as the primary artifact latest-paper-delivery, and the runtime only scans {run_dir}/outputs/, so a manifest written anywhere else is invisible. Close per the Final Checklist.

json
{ "paper_tex": "", "paper_pdf": "", "references_bib": "", "sections": [], "verified": false, "open_items": [] }

Pre-load (before execution)

1. Codebase docs: If .workflow/codebase/ARCHITECTURE.md exists, read for project context
2. Specs: maestro load --type spec --category coding — load coding conventions
3. Wiki knowledge: maestro search "academic writing research paper" --json — top 5 entries as prior context
4. All optional — proceed without if unavailable

Architecture Overview

User: "Write a paper from this repo"
         |
         v
┌──────────────────────────────────────────────────────────────────────┐
│  SKILL.md (Orchestrator)                                             │
│  Collect preferences → Dispatch phases → Track progress              │
└──────────┬───────────────────────────────────────────────────────────┘
           |
   ┌───────┼───────┬───────────┬──────────┬──────────┬────────────┐
   v       v       v           v          v          v            v
┌──────┐┌──────┐┌──────────┐┌──────────┐┌──────────┐┌──────────────┐
│ P1   ││ P2   ││ P3       ││ P4       ││ P5       ││ P6           │
│ Repo ││Struct││ Section  ││ Citation ││ Anti-AI  ││ Conference   │
│ Under││Plan  ││ Drafting ││ Manage   ││ Polish   ││ Formatting   │
└──┬───┘└──┬───┘└────┬─────┘└────┬─────┘└────┬─────┘└──────┬───────┘
   │       │         │           │           │             │
   v       v         v           v           v             v
 repo    outline   full draft   verified    polished     paper.tex
 context  + plan               .bib file   prose        (camera-ready)

Key Design Principles

1. Proactive drafting: Deliver complete drafts, then iterate on feedback. Do not block on every section.
2. Never hallucinate citations: Every citation must be verified via WebSearch and Google Scholar. Mark unverifiable references as [CITATION NEEDED].
3. Narrative-first writing: A paper is a story with one clear contribution. Define the What/Why/So What before writing.
4. Anti-AI polish is mandatory: All prose passes through pattern detection and humanization before final output.
5. Conference-aware from start: Target venue influences page limits, required sections, and framing.

Interactive Preference Collection

Before dispatching to any phase, collect these preferences:

Questions to ask the user:

1. Research Repository
   "Where is the research repo? (path or URL)"
   → repoPath

2. Target Conference
   Options: NeurIPS | ICML | ICLR | ACL | AAAI | COLM | Other
   → targetConference

3. Paper Type
   Options: Full Paper | Short Paper | Workshop Paper
   → paperType

4. Output Directory
   "Where should the paper be written? (default: ./paper/)"
   → outputDir

5. Existing Materials
   "Any existing drafts, notes, or outlines to build on? (path or 'none')"
   → existingMaterials

6. Writing Language
   Options: English | Chinese | Bilingual
   → writingLanguage

Store responses as paperPreferences context for all phases.

Auto Mode Defaults

When workflowPreferences.autoYes === true:

• Use detected repo path from cwd
• Default to NeurIPS format, Full Paper, English
• Output to ./paper/
• Skip confirmation prompts within phases

Execution Flow

> COMPACT DIRECTIVE: Context compression MUST check TodoWrite phase status. > The phase currently marked in_progress is the active execution phase -- preserve its FULL content. > Only compress phases marked completed or pending.

TodoWrite Setup

Paper Writing Workflow:
- [ ] Phase 1: Repo Understanding — explore repo, identify contribution
- [ ] Phase 2: Structure Planning — plan outline, define narrative
- [ ] Phase 3: Section Drafting — write all sections
- [ ] Phase 4: Citation Management — find, verify, format citations
- [ ] Phase 5: Anti-AI Polish — remove AI patterns, humanize prose
- [ ] Phase 6: Conference Formatting — apply template, compile

Phase Sequence

Phase 1: Repo Understanding
   └─ Ref: phases/01-repo-understanding.md
      ├─ Input: repoPath, existingMaterials
      └─ Output: repoContext (contribution, results, existing citations)

Phase 2: Structure Planning
   └─ Ref: phases/02-structure-planning.md
      ├─ Input: repoContext, targetConference, paperType
      └─ Output: paperOutline (section plan, narrative arc, page budget)

Phase 3: Section Drafting
   └─ Ref: phases/03-section-drafting.md
      ├─ Input: repoContext, paperOutline, writingLanguage
      └─ Output: draftSections (all sections as LaTeX content)

Phase 4: Citation Management
   └─ Ref: phases/04-citation-management.md
      ├─ Input: draftSections, repoContext.existingCitations
      └─ Output: verifiedBib (references.bib), updatedDraft (citations resolved)

Phase 5: Anti-AI Polish
   └─ Ref: phases/05-anti-ai-polish.md
      ├─ Input: updatedDraft
      └─ Output: polishedDraft (humanized prose, AI patterns removed)

Phase 6: Conference Formatting
   └─ Ref: phases/06-conference-formatting.md
      ├─ Input: polishedDraft, verifiedBib, targetConference
      └─ Output: paper.tex (complete manuscript ready for compilation)

Phase Reference Documents (read on-demand when phase executes):

| Phase | Document | Purpose | Compact | |-------|----------|---------|---------| | 1 | phases/01-repo-understanding.md | Explore repo, identify contribution | TodoWrite driven | | 2 | phases/02-structure-planning.md | Plan outline, define narrative | TodoWrite driven | | 3 | phases/03-section-drafting.md | Write all paper sections | TodoWrite driven + sentinel | | 4 | phases/04-citation-management.md | Find, verify, format citations | TodoWrite driven + sentinel | | 5 | phases/05-anti-ai-polish.md | Remove AI patterns, humanize | TodoWrite driven + sentinel | | 6 | phases/06-conference-formatting.md | Apply template, compile | TodoWrite driven |

Compact Rules:

1. TodoWrite in_progress → preserve full content, do not compress
2. TodoWrite completed → may compress to summary
3. sentinel fallback → phases marked with sentinel contain compact sentinel; if only sentinel remains after compression, must immediately Read() to recover before continuing

Core Rules

1. Citation integrity: NEVER generate BibTeX from memory. Always verify via WebSearch + Google Scholar. Mark unverifiable as [CITATION NEEDED].
2. One contribution: The paper tells one story. Every section supports the central narrative.
3. Proactive delivery: Write full drafts, flag uncertainties. Do not block waiting for per-section approval.
4. Conference compliance: Respect page limits, required sections, and anonymization requirements.
5. Anti-AI mandatory: All prose must pass anti-AI pattern detection before final output.

Input Processing

User input is parsed into paperPreferences:

REPO: [path to research repository]
CONFERENCE: [NeurIPS | ICML | ICLR | ACL | AAAI | COLM]
TYPE: [Full | Short | Workshop]
OUTPUT: [output directory path]
MATERIALS: [path to existing drafts or 'none']
LANGUAGE: [English | Chinese | Bilingual]

If user provides free text like "write a paper about my transformer project", extract:

• Repo path from context or ask
• Default conference to NeurIPS
• Default type to Full Paper
• Default language to English

Data Flow

Phase 1 ──repoContext──→ Phase 2
Phase 2 ──paperOutline──→ Phase 3
Phase 1 ──repoContext──→ Phase 3
Phase 3 ──draftSections──→ Phase 4
Phase 4 ──updatedDraft + verifiedBib──→ Phase 5
Phase 5 ──polishedDraft──→ Phase 6
Phase 4 ──verifiedBib──→ Phase 6

Data persistence: The paper artifacts live in outputDir/ — a working area in the
user's repo (analogous to source code), NOT the Run truth source. The Run records
synthesis + a delivery manifest (see Run Lifecycle above).

  outputDir/.writing/            (paper workspace, user-owned)
  ├── repo-context.md        (Phase 1 output)
  ├── paper-outline.md       (Phase 2 output)
  ├── drafts/                (Phase 3 output)
  │   ├── abstract.tex
  │   ├── introduction.tex
  │   ├── methods.tex
  │   ├── experiments.tex
  │   ├── related-work.tex
  │   ├── conclusion.tex
  │   └── appendix.tex
  ├── references.bib         (Phase 4 output)
  ├── polished/              (Phase 5 output)
  │   └── (same structure as drafts/)
  └── paper.tex              (Phase 6 output)

  {run_dir}/report.md            (workflow synthesis + delivery manifest)
  {run_dir}/outputs/             (delivery-paths list pointing into outputDir/)

TodoWrite Pattern

Phase Start (Attach)

When Phase N begins:
  → Mark Phase N as in_progress in TodoWrite
  → Add sub-tasks for Phase N steps
  → Execute sub-tasks sequentially

Phase End (Collapse)

When Phase N completes:
  → Mark all Phase N sub-tasks as completed
  → Collapse to summary: "Phase N complete: [key output]"
  → Mark Phase N+1 as in_progress

Post-Phase Updates

Between phases, update a running paper-notes document:

markdown
# Paper Writing Notes (accumulated)

## Contribution (Phase 1)
[One-sentence contribution statement]

## Outline (Phase 2)
[Section structure with page budgets]

## Draft Status (Phase 3)
[Section completion status]

## Citation Status (Phase 4)
[Verified count / placeholder count]

## Polish Status (Phase 5)
[Anti-AI score per section]

Written to: outputDir/.writing/paper-notes.md

Error Handling

| Error | Action | |-------|--------| | Repo path invalid | Ask user for correct path | | Cannot identify contribution | Present top 3 candidates, ask user to choose | | Citation not found | Mark [CITATION NEEDED], continue, report at end | | LaTeX compilation fails | Fix common errors (missing packages, encoding), retry once | | Anti-AI score below 35 | Re-polish section, flag for manual review | | Page limit exceeded | Suggest specific cuts (move proofs to appendix, condense related work) |

Coordinator Checklist

Before Each Phase

• ] Previous phase output exists and is valid
• ] TodoWrite updated (current phase in_progress)
• ] Required inputs available

After Each Phase

• ] Output files written to outputDir/.writing/
• ] paper-notes.md updated
• ] TodoWrite collapsed (phase completed)
• ] User notified of phase completion and key decisions made

Final Checklist

• ] All 6 phases completed
• ] {run_dir}/outputs/delivery.json written (primary artifact — run check cannot register the delivery without it)
• ] paper.tex compiles without errors
• ] All citations verified (no remaining [CITATION NEEDED])
• ] Anti-AI score >= 35 for all sections
• ] Page limit respected
• ] Anonymization applied (for blind review)
• ] Conference checklist completed (if required)

Related Skills

• scholar-ideation: Use before this skill to develop research ideas
• scholar-experiment: Use before this skill to run experiments
• scholar-review: Use after this skill to review/revise the paper