Academic Manuscript Writing

Academic Manuscript Lifecycle Writing

Write and revise manuscripts according to their actual lifecycle stage. Own the manuscript argument, prose, revision scope, response-letter content, and handoff to final submission; route evidence, citations, statistics, figures, documents, and portal actions to the appropriate specialist without surrendering narrative control.

Respect authority and evidence

1. Follow the user, applicable AGENTS.md, project rules, PAPER.md, venue requirements, and evidence hierarchy. This skill never upgrades unverified notes into paper facts.
2. Identify the canonical manuscript source and rendered reference before editing. Preserve unrelated author changes and protected historical/submitted versions.
3. The main agent owns stage selection, mainline, claim/evidence alignment, canonical-file integration, and final prose. A specialist or subagent cannot enlarge the authorized mutation scope.
4. Never invent results, citations, table/figure locations, reviewer requirements, declarations, or completion states. Use needs_verification when evidence is missing.
5. External workflow-tool disclosure remains separately controlled by applicable project rules and the final-submission audit. This skill must not add, retain, remove, translate, or relocate such disclosure without the required author approval.
6. For claim-bearing work, consume the bounded evidence packet produced by the research lifecycle: claim ID/scope, canonical experiment card and raw source, or a claim_verified project literature note with exact location. Do not treat the global paper catalog, a project tag, a completed run, or fluent existing prose as verified evidence. Route new or broadened claims back to the owning literature/experiment workflow before writing them as findings.

Select the manuscript stage first

Use stage-router.md to identify the current stage, reusing an unchanged router and established stage contract already in context. Assign exactly one stage:

initial_draft / manuscript_polish / pre_submission_audit / major_revision_preserving / minor_revision_local / final_submission_audit / proof_correction

State the detected stage and mutation scope briefly before substantive work. If the evidence supports multiple stages, use the least mutating safe stage and follow the transition gates; do not combine drafting, auditing, revision, and final submission into one uncontrolled pass.

Separate completion of the requested task from completion of the entire manuscript stage. A bounded paragraph edit, local response draft, or formatting question does not require a full manuscript audit, new mainline card, or all stage deliverables. Reuse relevant existing records, preserve scientific meaning, and verify changed claims when needed. Apply full stage-completion gates only when completing or advancing that stage; do not label a local edit as stage completion.

Load only the relevant writing rules

• For initial_draft, manuscript_polish, or pre_submission_audit, read writing-standards.md.
• For major_revision_preserving or minor_revision_local, read revision-and-response.md. Also read writing-standards.md when changing scientific exposition, argument, citations or figure/table discussion; a spelling-only correction does not need that additional reference.
• For final_submission_audit, read submission-handoff.md, then use the sci-research-manager final-submission audit.
• For proof_correction, read the proof section in submission-handoff.md.

Do not load every reference when only one stage applies.

Consolidated manuscript owner

This skill contains the maintained, stage-aware writing standards for this package. Earlier generic drafting, polishing, response, self-review, and chapter-writing flows are consolidated here and are not parallel workflow owners. Do not reconstruct a multi-owner writing chain.

Preserve the useful separation of roles inside this single lifecycle: draft from evidence, polish without changing meaning, audit without editing, revise against the submitted base, and hand frozen content to final submission control. A request for several deliverables does not collapse these roles into one uncontrolled rewrite.

Specialist skills remain appropriate for bounded work:

• literature search and source verification;
• citation placement and bibliography validation;
• statistical analysis and quantitative validation;
• scientific figures and charts;
• data/code availability;
• LaTeX, Word, PDF, spreadsheet, and presentation production;
• read-only reviewer simulation;
• browser or portal operation after separate authorization.

Use the selected stage's specialist boundaries; do not reread the unchanged router before each handoff. Invoke only the smallest set that changes the outcome. A typed handback returns to the current primary agent, not another automatically spawned owner.

Use a two-tier contract: this skill is the sole manuscript owner, while each specialist receives a bounded input and returns one typed artifact such as a verified source packet, statistical result, quantitative plot, method diagram, compiled document, or mock-referee report. Specialists must not rewrite surrounding prose, change the selected manuscript stage, expand the revision scope, promote evidence, or integrate directly into the canonical manuscript. The main agent checks the handback and performs the final integration.

For path compatibility, existing projects may still link workflow.md, section-playbooks.md, evidence-chain.md, figure-table-writing.md, style-rules.md, or examples.md. Treat them as secondary reference material only; the stage router and stage-specific references above govern any conflict. Do not load them unless the user or an existing project explicitly points to them.

Required stage artifacts

For a whole-stage task, maintain the applicable artifacts below; for a bounded subtask, update only the affected existing records:

• canonical source/render identity;
• mainline card after the initial-draft stage;
• claim/evidence and terminology records when the project uses them;
• issue list for pre-submission audit;
• submitted-base identity, comment matrix, preservation report, unrequested-change report, clean/marked-up pair, and response for revisions;
• package inventory and final-audit report for submission;
• correction list and verified proof for production.

Do not create duplicate manuscript trees, decorative indexes, or a new permanent template when the project already has one.

Close the stage

Use the completion and transition gates in stage-router.md. Report:

1. detected and completed stage;
2. canonical inputs and evidence used;
3. manuscript, response, figure/table, or package changes;
4. checks performed;
5. unresolved blockers and the only valid next stages.

Do not claim a stage is complete merely because prose was generated or a PDF compiled.