paper-from-zero

name	paper-from-zero
description	Route a fixed research topic into a rigorous paper-generation workflow. Handles active literature search, innovation framing, contribution/evidence planning, and routes to either the review writer or empirical writer skill.
metadata	{"short-description":"Research-to-paper router for review and empirical papers"}

Paper-From-Zero

Use this skill when the user already has a topic/domain and wants a structured path from topic -> innovation framing -> evidence plan -> draft-ready paper workflow.

This skill is the front door of the paper stack:

• It decides whether the work is best treated as a review or empirical paper.
• It actively searches literature and frames the contribution.
• It produces the handoff contract used by the downstream writer skill.

When to Use

• The topic is known, but the paper structure and contribution are not yet pinned down.
• The user wants the model to search for candidate innovation angles.
• The user wants a rigorous pre-writing stage before draft generation.

When NOT to Use

• The user already has a finished review outline and only wants review execution.
• The user already has an experimental paper contract and only wants draft execution.
• The task is non-academic or does not need citation-grounded writing.

Outputs

• brief/topic-brief.md
• brief/contribution-map.yaml
• brief/evidence-matrix.csv
• notes/innovation/ (innovation candidates + evidence links; recommended)
• plan/outline-contract.md
• plan/router-decision.md
• A routing decision to one downstream writer:
  • ../arxiv-paper-writer/SKILL.md for review papers
  • ../empirical-paper-writer/SKILL.md for experimental papers

Workflow

1. Confirm the topic, constraints, and whether the user already has a preferred innovation.
2. Actively search literature and build a compact literature map.
3. Produce 3-5 candidate innovation/contribution framings unless the user already supplied one.
4. Kill weak framings early: reject ideas that lack a clear gap, evidence path, or falsifiable claim.
5. Build a contribution map:
   • primary claim
   • secondary claims
   • non-goals / out-of-scope claims
   • risk factors / likely reviewer objections
6. Build an evidence matrix for every claim:
   • required citations
   • required visuals/tables
   • required experiments (if any)
   • what may remain placeholder vs what must be verified before finalization
7. Produce an outline contract with section goals, citation quotas, and figure quotas.
8. Route:
   • review -> use ../arxiv-paper-writer/SKILL.md
   • empirical -> use ../empirical-paper-writer/SKILL.md

Collaboration Hooks (Recommended)

The following hooks integrate the breadth (Gemini) and depth (Claude) co-pilots at fixed points in the workflow. Hooks are optional but strongly recommended for research rigor.

#	Trigger	Call	Input	Output consumed by
1	After step 2 (literature initial screening)	Gemini literature-map	topic + Key Terms from topic-brief	Candidate papers and keyword clusters feed back into literature search; not written directly into artifacts.
2	After step 5 (contribution-map initial draft)	Claude claim-stress-test	contribution-map.yaml full text	risks and reviewer_objections feed back into contribution-map revision.
3	After step 6 (evidence-matrix initial draft)	Gemini evidence-matrix-gap-check OR Claude evidence-sufficiency-audit	evidence-matrix.csv + claims list	Gap list or sufficiency assessment feeds back into evidence-matrix revision.
4	Before step 8 (routing decision)	Claude route-review-vs-empirical	contribution-map + evidence-matrix summary	Routing recommendation + adversarial challenge written into router-decision.md.

Hooks are non-blocking. If the target model is unavailable, the orchestrator decides the fallback. Candidates-Only constraint applies regardless of executor.

Hook 3 selection rule: If the average evidence rows per claim < 3, call Gemini evidence-matrix-gap-check first (breadth). If coverage appears sufficient, call Claude evidence-sufficiency-audit (depth). Both may be called sequentially.

Constraint: Collaboration outputs are inputs to artifact revision, not direct writes. All candidate entries must pass the Candidates-Only constraint defined in the co-pilot skills. validate_handoff.py does not check capsule state — it only validates final artifact completeness.

Routing Rules

• Route to review when the deliverable is a survey, synthesis, taxonomy, benchmark-style review, or evidence-first overview.
• Route to empirical when the deliverable makes a novel method/setting/evaluation claim that needs experimental validation.
• If the topic contains both, prefer the paper’s primary contribution type.

Handoff Contract

Before routing, create the following artifacts in the target project folder:

• brief/topic-brief.md: topic, scope, audience, constraints, venue/page targets
• brief/contribution-map.yaml: claims, non-claims, novelty framing, risks
• brief/evidence-matrix.csv: claim-to-evidence mapping
• plan/outline-contract.md: section tree + section intent + citation/figure quotas
• plan/router-decision.md: chosen mode and why

The downstream writer must consume these artifacts rather than re-guessing user intent.

Validation (recommended)

Before routing, validate the handoff artifacts:

python3 .codex/skills/paper-from-zero/validate_handoff.py --project-dir <paper_dir>

Strictness Rules

• Do not invent novelty. Frame novelty as a hypothesis until grounded by evidence.
• Do not skip literature search for “obvious” topics.
• Do not allow claim language stronger than available evidence.
• For empirical work, explicitly separate planned, placeholder, and verified results.

References to Read

• references/architecture.md
• references/innovation-framing.md
• references/routing-policy.md