Research paper plan

Research Paper Plan

Quick start

1. Start from supported claims, not from section titles.
2. Decide whether this is a standalone paper plan or the paper stage inside an orchestrated suite.
3. Initialize paper-plan.md, claims-evidence-matrix.md, figure-plan.md, and citation-plan.md only when tracked outputs will help.
4. Block on missing evidence instead of writing around it.
5. Plan figures, citations, and limitations as first-class parts of the manuscript story.

Modes

Standalone mode

• Work from the user prompt plus any local claims, results, notes, or drafts already present.
• Do not require a suite root.
• Collaboration is still allowed: if novelty review, experiment plan, results audit, or review-loop artifacts exist, use them; if another skill would materially improve the manuscript plan, recommend or invoke it.

Orchestrated mode

• Prefer the canonical directory ./paper-plan/.
• Read upstream context from research-brief.md, artifact-index.md, ./novelty-review/, ./experiment-plan/, ./review-loop/, and ./zotero/ when present.
• Keep the paper outputs legible to later drafting and review passes.

Input contract

• Minimum:
  • one or more claims the paper wants the reader to accept
  • evidence or source artifacts that support those claims
• Prefer:
  • target venue or audience
  • known weaknesses or reviewer objections
  • desired exhibit list
  • existing novelty, experiment, results-audit, or review-loop artifacts
  • existing Zotero exports or library artifacts

Hard stops

• Stop if the user wants a paper plan but there is no credible evidence behind the main claim.
• Stop if claims outrun the available artifacts and the gap cannot be made explicit.
• Stop if the venue constraints matter but remain unknown.
• In standalone mode, do not create excess structure when a compact direct outline is enough.

Output contract

• Primary files:
  • paper-plan.md
  • claims-evidence-matrix.md
  • figure-plan.md
  • citation-plan.md
• In orchestrated mode, these live under ./paper-plan/.
• In standalone mode, any target directory is valid.

Workflow

1) Freeze the supported claims

• Use references/claims-evidence-matrix-template.md.
• Separate:
  • main contribution claims
  • supporting claims
  • limitation claims
• Downgrade or remove claims that do not have a clear evidence path.

2) Fit the paper shape to the evidence

• Use references/paper-outline-template.md, references/section-archetypes.md, and references/venue-adapters.md.
• Choose a structure that matches what the evidence can actually support.
• Treat page budget and venue expectations as constraints, not afterthoughts.

3) Plan exhibits deliberately

• Use references/exhibit-plan-checklist.md.
• Every figure and table should answer a paper question or defend a claim.
• Mark exhibits as:
  • mandatory
  • helpful
  • cut

4) Build the citation plan carefully

• Use references/citation-verification-rules.md.
• If a Zotero library already exists for the project, invoke research-zotero or consume ./zotero/ artifacts before inventing citation structure from memory.
• Record which claims need citations versus which require empirical evidence.
• Keep citation verification explicit instead of inventing references from memory.

5) Keep collaboration open

• Pull in research-results-auditor when the evidence quality is unclear.
• Pull in research-review-loop when the story needs an adversarial pass.
• Pull in research-novelty-review when positioning remains unstable.
• Pull in research-zotero when citation grounding, BibTeX export, or CSL-JSON export would materially improve the paper plan.
• Missing evidence remains a block in every mode. Do not write unsupported paper stories.

References

• references/paper-outline-template.md
• references/claims-evidence-matrix-template.md
• references/section-archetypes.md
• references/venue-adapters.md
• references/exhibit-plan-checklist.md
• references/citation-verification-rules.md
• references/tabmol-ddi-ood-adapter.md

Script

• scripts/init_paper_pack.py: create the core paper-planning files in a standalone directory or the suite's paper-plan/ directory.