--- name: docxology/template-academic-paper source: https://app.decimal.ai/s/docxology-template-academic-paper@1/SKILL.md source_sha256: 51e9af7aad69 --- # Academic paper Template-native paper workflow. It uses project manuscript sources, generated variables, validation gates, and evidence registries rather than a copied external academic agent prompt. ## Natural invoke - "Help me plan this paper" - "Write the outline and methods section from these artifacts" - "Revise the manuscript after reviewer comments" - "Check citations and convert the final paper format" - "Write an AI-use disclosure tied to the repo evidence" ## Inputs to confirm - **Project** - resolve through `docs/_generated/active_projects.md`. - **Mode** - plan, outline, full, revision, format, citation-check, prose-quality, or disclosure. - **Manuscript style** - Pandoc-crossref or registry tokens; do not mix styles. - **Evidence sources** - generated variables, claim ledger, figures, tables, references, validation reports. ## Workflow 1. **Plan first when uncertain** - capture target venue, paper type, contribution, section map, and unresolved material gaps. 2. **Draft from artifacts** - write against `projects//manuscript/`, generated variables, figure captions, and citekeys; use `[MATERIAL GAP]` instead of fabricating missing evidence. 3. **Preserve injected values** - prefer `[[VAR:...]]`, registry-backed labels, citekeys, and project-defined cross-reference tokens over hard-coded numbers. 4. **Validate continuously** - run prerender, markdown, citation, PDF, and integrity checks appropriate to the mode. 5. **Self-edit the prose** - run the AI-writing-fingerprint scan (`prose-quality`) and tighten any flagged stock phrasing, em-dash over-use, or uniform sentence length. Treat it as advisory (revise, do not blindly delete); it is a deterministic clean-room distillation of the ARS writing-quality check, not a model judgment. 6. **Verify references exist** - in citation-check/format/finalize, run the reference-existence gate so no cited DOI/arXiv id is fabricated and no metadata is mismatched. 7. **Handoff for review** - use [academic-paper-reviewer](../academic-paper-reviewer/SKILL.md) for read-only critique; use claim verification before finalization. ## Deliverables - Plan mode: section outline, evidence map, unresolved gaps, and commands to validate. - Full/revision mode: source-layer manuscript edits, response notes, and validation status. - Format/citation mode: citation audit, render-safe changes, and output paths. - Disclosure mode: concise AI-use disclosure grounded in project evidence and human review checkpoints. ## Verification commands ```bash uv run python -m infrastructure.validation.cli prerender projects//manuscript --repo-root . uv run python -m infrastructure.reference.citation validate projects//manuscript/references.bib uv run python -m infrastructure.reference.verification verify projects//manuscript/references.bib --live --as-of-year uv run python -m infrastructure.validation.cli prose-quality projects//manuscript uv run python -m infrastructure.validation.cli markdown projects//manuscript --repo-root . --strict uv run python -m infrastructure.validation.cli integrity output// ``` ## References - [MODE_REGISTRY.md](../MODE_REGISTRY.md) - [manuscript-creation](../manuscript-creation/SKILL.md) - [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md)