Workflow 3: Paper Writing Pipeline

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.

In this hybrid pack, the pipeline itself is unchanged, but paper-plan and paper-write use Orchestra-adapted shared references for stronger story framing and prose guidance.

Constants

• VENUE = ICLR — Target venue. Options: ICLR, NeurIPS, ICML, CVPR, ACL, AAAI, ACM, IEEE_JOURNAL (IEEE Transactions / Letters), IEEE_CONF (IEEE conferences). Affects style file, page limit, citation format.
• MAX_IMPROVEMENT_ROUNDS = 2 — Number of review→fix→recompile rounds in the improvement loop.
• REVIEWER_MODEL = gpt-5.4 — Model used via Codex MCP for plan review, figure review, writing review, and 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.
• ILLUSTRATION = figurespec — Architecture/illustration generator for Phase 2b: figurespec (default, deterministic JSON→SVG via /figure-spec, best for architecture/workflow/topology), gemini (AI-generated via /paper-illustration, best for qualitative method illustrations; needs GEMINI_API_KEY), codex-image2 (AI-generated via /paper-illustration-image2 through the local Codex native image bridge — no external API key, uses your ChatGPT Plus/Pro quota; experimental), mermaid (Mermaid syntax via /mermaid-diagram, free, best for flowcharts), or false (skip Phase 2b, manual only).

Override inline: /paper-writing "NARRATIVE_REPORT.md" — venue: NeurIPS, illustration: gemini, human checkpoint: true IEEE example: /paper-writing "NARRATIVE_REPORT.md" — venue: IEEE_JOURNAL

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.

Optional: Style reference (— style-ref: <source>, opt-in)

Lets the user steer structural style (section ordering, theorem density, sentence cadence, figure density, bibliography style) of the generated paper toward a reference paper they admire. Default OFF — when the user does not pass — style-ref, do nothing differently from before.

When — style-ref: <source> is in $ARGUMENTS, run the helper FIRST, before Phase 1 (paper-plan):

if [ ! -f tools/extract_paper_style.py ]; then
  echo "error: tools/extract_paper_style.py not found — re-run 'bash tools/install_aris.sh' to refresh the '.aris/tools' symlink (added in #174), or copy the helper manually from the ARIS repo" >&2
  exit 1
fi
CACHE=$(python3 tools/extract_paper_style.py --source "<source>")
case $? in
  0) ;;                                       # share $CACHE/style_profile.md with downstream WRITER phases only
  2) echo "warning: style-ref skipped (missing optional dep)" >&2 ;;
  3) echo "error: --style-ref source failed; aborting pipeline" >&2 ; exit 1 ;;
  *) echo "error: helper failed unexpectedly; aborting pipeline" >&2 ; exit 1 ;;
esac

Then forward — style-ref: <source> only to the writer-side sub-skills:

• /paper-plan (Phase 1) — outline structure
• /paper-write (Phase 3) — section-by-section prose
• /paper-illustration (Phase 2b) — figure structural matching, optional

Sources accepted: local TeX dir / file, local PDF, arXiv id, http(s) URL. Overleaf URLs/IDs are rejected — clone via /overleaf-sync setup <id> first and pass the local clone path.

Strict rules (full contract in tools/extract_paper_style.py docstring):

• Use style_profile.md as structural guidance only. Match section-count tendency, theorem density, caption-length distribution, sentence cadence, math display ratio, citation style.
• Never copy prose, claims, examples, or terminology from anything reachable through the cache.
• Never pass — style-ref (or the cache contents) to reviewer / auditor sub-skills — Phase 4.5 (/proof-checker), Phase 4.7 / 5.5 (/paper-claim-audit), Phase 5 (/auto-paper-improvement-loop reviewer), Phase 5.8 (/citation-audit) MUST run on the artifact alone. Cross-model review independence (../shared-references/reviewer-independence.md).

Pipeline

Phase 0: Assurance Setup

Resolve the active assurance level and persist it so Phase 6's external verifier reads the same value. Run once at pipeline start, before Phase 1.

Resolution order (first match wins):

1. Explicit — assurance: draft | submission in $ARGUMENTS
2. Derived from — effort:
   • lite / balanced → draft (default, zero change from current behavior)
   • max / beast → submission
3. Default: draft

Action:

mkdir -p paper/.aris
echo "<resolved-level>" > paper/.aris/assurance.txt   # draft or submission

What each level does downstream:

• draft — Existing behavior. Audits run only when their content detector matches (Phase 4.5 / 4.7 / 5.5 / 5.8). Missing artifacts are non-blocking. Silent-skip allowed.
• submission — The three mandatory audits (proof-checker, paper-claim-audit, citation-audit) are treated as load-bearing gates. Each sub-audit must emit its JSON artifact (PASS / WARN / FAIL / NOT_APPLICABLE / BLOCKED / ERROR) — never silent-skip. Phase 6 runs tools/verify_paper_audits.sh; a non-zero exit blocks the Final Report.

Escape hatch: a user wanting the old "beast = depth-only, no audit gate" can pass — effort: beast, assurance: draft explicitly. Legal but discouraged for actual submissions. See shared-references/assurance-contract.md for the full contract.

Announce the resolved level in-line before Phase 1:

📋 Assurance: <level> (derived from effort: <effort>)
   <either "current behavior, no audit gate" OR "mandatory audits gated by tools/verify_paper_audits.sh">

Phase 1: Paper Plan

Invoke /paper-plan to create the structural outline:

/paper-plan "$ARGUMENTS"

If — style-ref: <source> was passed in $ARGUMENTS and the helper succeeded above, append — style-ref: <source> to the invocation: /paper-plan "<topic> — style-ref: <source>". (Writer-side phase — forwarding is allowed; reviewer/auditor phases below must not see the style ref.)

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
• GPT-5.4 reviews the plan for completeness

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 p