Paper Spine

PaperSpine Orchestrator

Use this skill as the suite entrypoint. PaperSpine exposes one main skill: paper-spine. Each stage is executed by reading the corresponding playbook under references/.

Update detection: If the user asks to update, upgrade, check for updates, or configure automatic updates, read references/update.md and execute without starting intake or the writing workflow. Automatic updates are opt-in only.

Command Routing

Automatic Update Preflight

Before every normal workflow launch or resume, follow references/update.md and run the installed updater with --auto. The preflight is a local no-op unless the user has explicitly enabled automatic updates and the configured interval is due. Never enable it on the user's behalf.

If the preflight installs a new version, stop before intake/research/writing and ask the user to reload or restart the host, then invoke PaperSpine again. If the preflight fails, warn once and continue with the current installation; do not turn an update-network failure into a paper-workflow blocker.

For fine-grained stage execution, the orchestrator reads the playbook for each stage from references/ rather than requiring a separate skill invocation:

Historical worker skill names (paper-spine-research, etc.) are legacy only and are not user entry points.

Operating Principle

PaperSpine is a research-writing workflow, not a prose patcher. Its job is to learn the target scene and available evidence, confirm the controlling contribution and motivation, then give the writing Agent room to design the strongest argument and manuscript structure for the actual material.

Never fabricate data, metrics, p-values, datasets, citations, figures, or experimental claims. User materials are authoritative for this paper's results. External examples teach structure and rhetoric only.

Keep scientific boundaries explicit without repeating the full provenance disclaimer in every paragraph. Define stable evidence scope at the paper or section boundary, inherit it until the evidence changes, and restate only the exception. This preserves caution without defensive repetition.

Default to review_policy=balanced. Gates are decision aids, not a substitute for writing judgment. Hard-block fabricated facts/citations, unsupported primary claims, unresolved figure/text conflicts, broken citations, missing required metadata, and unusable deliverables. Treat stylistic preferences, literature breadth inside a declared closed corpus, optional planning forms, and minor review suggestions as advisory. Use strict only when the user requests it or the task is explicitly a submission/final-compliance audit. Read references/review-policy.md when selecting or changing this policy.

The internal evidence model may be precise; the manuscript should still sound like a confident scholarly article. Read references/assertive-scientific-writing.md: state supported results directly, reserve hedging for genuine uncertainty or causal/generalization boundaries, and do not repeat audit language in reader-facing prose.

Editorial North Star

The manuscript is the product; plans, ledgers, reviews, and receipts exist only to help the Agent write it. A workflow is not complete merely because its internal artifacts pass. The final paper must let its intended reader follow one visible arc: why the work was needed, what was done, what the evidence shows, what those findings mean, and what conclusion the evidence earns.

Give the writing Agent freedom to choose section architecture, paragraph moves, emphasis, and revision order from the confirmed contribution, target venue, and available evidence. Guide with reader questions and editorial judgment rather than paragraph quotas or extra forms. Hard stops are reserved for truth, authorization, unresolved evidence/figure identity conflicts, and unusable deliverables.

tier changes research and process depth, never the promised manuscript scale. A flash journal paper is still a complete journal paper; it is not permission to omit the ending, compress Results into captions, or replace Discussion with an audit summary. Read references/editorial-completeness.md before drafting and again for the integrated editorial pass.

Contribution-First, Reviewer-Aware Rules (V4)

These three rules sit above the motivation thread. Motivation remains required, but it supports the contribution rather than replacing it.

1. Contribution-First. The manuscript's highest-priority organizing unit is the confirmed contribution. Do not begin substantive writing until confirmed_contribution.md exists (what the paper adds, what problem/gap/ challenge makes it necessary, what evidence validates it, what claim boundary to respect, why a reviewer should find it publishable). Template + per-section checklists: references/contribution.md. Gate: contribution_check.py.
2. Results-as-Validation. Each major Results subsection must validate at least one contribution promise; metric-only units with no contribution mapping are a failure. Record this in results_validation.md. Template: references/results-validation.md. Gate: results_validation_check.py (journal / conference / competition scenes).
3. Reviewer-Aware. Before claiming submission-ready, create reviewer_audit.md (reviewer value map + objection register + editorial fit), populating the objection register from the three structured_review reviewer agents. Template: references/reviewer-audit.md. Gate: reviewer_audit_check.py.

The contribution check runs at semantic confirmation and again at planning; Results validation runs at planning before prose; reviewer audit runs before LaTeX assembly. Stage 12 re-runs all three as defense in depth. Final audit must never be the first place one of these failures is discovered.

User-Facing Language

When the user writes in Chinese, ui_language=zh, output_language=zh, or translation_package=zh, all user-facing communication must be in Chinese throughout the whole run, not only in the final completion report. This includes intermediate progress updates, status bullets, tool-result summaries, blocked messages, gate re-run notes, final delivery tables, and error explanations.

Do not write English progress sentences such as "Chinese .docx generated", "Now writing the word report", "All stages passed", "Deliverables", or "PaperSpine Workflow Complete" in those Chinese-facing runs. Use Chinese status phrases instead, for example:

• 中文 Word 文档已生成：final_paper/paper.zh.docx。正在写入 Word 检查报告并重新运行关卡检查。
• PaperSpine 工作流已完成
• 全部阶段已通过
• 交付文件清单

Tool names, file paths, command names, and required English manuscript text may remain literal, but explanatory prose around them must be Chinese.

Required Configuration

Prefer reading paper_rewriting_output/paper_spine_config.json. If it is missing, read references/intake.md and collect configuration.

Required fields:

Optional policy fields (default without adding intake questions):

Non-Negotiable Route

Resume-first rule: Before starting any workflow, read references/resume.md and run progress_check.py against paper_rewriting_output/. If earlier stages have produced valid artifacts, start from the first incomplete stage. After executing that stage, run its gate, run the full progress check again, and continue until final audit is complete. Do not restart from intake unless the user explicitly requests a clean run or the output directory is empty.

Anti-skip rule: Each stage is a gate. After completing a stage, run its gate check before moving to the next. If the gate fails, route back to that stage — do not skip, do not hand-write the missing artifact, do not patch downstream. The gate script is progress_check.py --gate <stage_name>. Never use bulk placeholder generators such as generate_artifacts.py, quick_generate.py, or mock_artifacts.py to replace real stage work.

Default Word output: Word (.docx) is a standard required artifact. Produce it in the LaTeX stage unless word_output is explicitly set to none in config. If pandoc is unavailable, write a BLOCKED/FAIL note in latex_report.md and do not declare completion.

Stage 1 — Intake / Configuration

If configuration is missing or incomplete, run the terminal wizard from the intake UI via the absolute installed launcher $env:USERPROFILE\.claude\skills\paper-spine\scripts\launch_paperspine_ui.ps1 (or the .codex equivalent, or $HOME/.codex/skills/paper-spine/scripts/launch_paperspine_ui.sh on bash); do not ask the user to hand-write JSON or answer a long plain chat checklist when a terminal is available. In Claude Code, /paperspine is the preferred entry: it launches the external intake window automatically when configuration is missing.

Codex hard constraint (do not skip): when paper_rewriting_output/paper_spine_config.json is missing, the FIRST tool action after reading this skill MUST be to run the absolute launch_paperspine_ui.ps1 (resolve under ~/.codex/skills/... or ~/.claude/skills/...) with sandbox_permissions: require_escalated so the window can open.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate intake

If FAILED: return to intake. Config must exist and be valid before any research.

Stage 2 — Research

Read references/research.md and execute the research stage. Research must index local references per reference_mode and reference_paths before any web collection.

Required outputs: reference_materials/source_index.md, research_dossier.md, exemplar_learning_dossier.md, style_profile.md, sota_gap_map.md, contribution_options_after_research.md, motivation_options_after_research.md.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate research

If FAILED: return to research. All six artifacts must exist before citation work begins.

Stage 3 — Citation Support Bank

Read references/citation.md and build citation_support_bank.md. Resolve the literature contract first. open_literature builds a broad candidate pool (normally citation_target_count * 3 unique sources, with recency as a coverage goal). closed_corpus exhausts and deduplicates the supplied bibliography, requires enough real sources for the planned final citations, and treats recency/breadth as disclosed limitations rather than reasons to stop writing. Repeating one paper never increases source coverage in either mode.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate citation

If FAILED: return to citation. The bank must exist with sufficient candidates.

Stage 4 — Semantic Confirmation

Read references/semantic-confirmation.md. Stop for user confirmation of the contribution contract first and its supporting motivation second. Write confirmed_contribution.md and confirmed_motivation.md only after the user chooses, revises, combines, or replaces the research-generated options.

This stage is BLOCKED (not just pending) until the user confirms both artifacts. Present contribution_options_after_research.md and motivation_options_after_research.md; do not auto-select either one.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate semantic_confirmation

If FAILED/BLOCKED: stop and wait for user. Do not proceed with an unconfirmed or invalid contribution contract, even when motivation is already confirmed.

Stage 5 — Humanize (if applicable)

If humanize_tier is light, medium, or heavy, read references/humanize.md and apply tier-specific constraints.

Stage 6 — Writing / Drafting

If workflow is rewrite_existing, read references/rewrite.md. If workflow is build_from_materials, read references/build.md.

Both workflows create section_blueprints.md before drafting. In balanced mode, the blueprint plus evidence ledger/results map are enough: the Agent may plan in the format that best supports the paper and should not expand a table merely to satisfy a row quota. writing_rationale_matrix.md is required only in strict mode or when the user explicitly asks for a paragraph-level rationale trace.

For evidence-bearing scenes, read references/scientific-evidence-ledger.md and create scientific_evidence_ledger.json during planning. Separate and link sources, claims, numeric facts, methods, outcomes, and results; preserve verification state rather than collapsing all evidence into one prose bank.

For journal, conference, and competition, read references/results-validation.md and create results_validation.md during planning, before Results prose. Every planned major Results unit must test at least one contribution promise.

When existing scientific figures are present or new/redesigned figures are needed, set figure_policy to existing_only or generate_or_redesign, read references/figure-story.md, and inspect every existing image and panel with a multimodal tool before drafting. Create one figure_requests.json contract that records each figure's question, dominant claim, intended conclusion, claim boundary, hero panel, panel jobs/evidence anchors, Results units, caption, and keep/redesign/create decision. This is both the manuscript storyboard and the PaperFigure/FigMirror handoff; do not add a second figure-planning form.

Read references/editorial-completeness.md. Use the blueprint and figure story as private scaffolding, then expand them into full reader-facing argument. The Agent may merge, split, or rename sections to fit the venue; every full-paper scene must nevertheless complete the research arc and give Results and Discussion enough space to do their distinct intellectual jobs.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate planning

If FAILED: return to the writing stage. Blueprints and, for evidence-bearing scenes, the Results validation/evidence map remain mandatory. Strict mode also requires the rationale matrix. Planning artifacts should capture real decisions, not restate the same justification in many cells.

Write Results by figure question and claim: visible evidence first, then the bounded answer. Do not reduce Results to chronological panel narration. For redesign/create, use the existing PaperFigure integration; its candidates must preserve the same scientific-story contract while exploring visual form.

After drafting, run:

python scripts/progress_check.py paper_rewriting_output --gate drafting

Stage 7 — Integrity Audit

Run structured_review.py. In balanced mode it prepares a compact editorial brief, then one capable Agent reads the actual manuscript and writes a free-form editor synthesis. Judge the paper as a reader: complete argument, Results depth, Discussion synthesis, figure/text reading order, and an earned ending. Do not manufacture reviewer personas, scores, rationale rows, or extra forms. Revise the manuscript, then mark the integrated review PASS only when the editor synthesis genuinely supports that judgment. Strict mode keeps three independent reviewer passes, phase receipts, reviewer_audit.md, and reviewer_audit_check.py.

Run before LaTeX assembly:

python scripts/structured_review.py paper_rewriting_output --markdown --write
python scripts/integrity_audit.py paper_rewriting_output --markdown --write

For strict mode, add structured_review.py --dispatch and reviewer_audit_check.py per references/review-policy.md. Review BLOCKER findings. Return to the relevant stage for any BLOCKED dimension. Do not proceed to LaTeX with unresolved BLOCKERs.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate integrity_audit

If FAILED: return to drafting or the owning upstream stage, fix BLOCKERs, and re-run structured review, reviewer audit, and integrity audit until the gate passes.

Stage 8 — LaTeX / PDF / Word

Read references/latex.md for LaTeX assembly, PDF compilation, and Word output. Word (.docx) is a standard required artifact. Produce and check it unless word_output is explicitly none.

After the current PDF and figure assets are final, read references/publication-surface.md and references/visual-readiness-gate.md. Scrub internal audit scaffolding, render every PDF page and figure, inspect the actual renders with a multimodal tool, complete visual_audit_manifest.json, and require visual_readiness_check.py PASS. TeX-source PASS does not imply visual_ready. For every scientific figure, compare the actual pixels against its story contract and record claim alignment, panel-role alignment, claim boundary, and panel-level receipts. If the final image disagrees with the planned story, revise the image or prose and invalidate the old receipt. Also inspect the paper in reading order. Figures should appear close enough to the Results units that interpret them for a reader to follow the argument; a hash-valid figure floated beyond its discussion is visually valid but editorially unresolved.

Citation mechanism (hard rule): Every in-text citation must be a real \cite{key} linked to a bibliography entry — either \bibliographystyle{unsrt} (or plain/ieeetr) + \bibliography{references.bib}, or a thebibliography block whose \bibitem{key} entries are reached by \cite{key}. Never type the bracket number as literal text: a hand-typed [1] is inert and does not link to the reference list (in the PDF or the .docx). A numeric bibliographystyle/CSL still renders as [1] or [3,12,13], so the visible plain-numeric style is preserved. Do not use author-year citations and do not wrap numeric citations in extra parentheses such as ([15]). latex_guard.py fails literal-bracket citations with no \cite and out-of-sync numbering; it also checks the format.

Title (hard rule): main.tex must contain \title{...} and \maketitle. Word output must begin with the paper title — not Abstract, Keywords, or body text. latex_guard.py checks the TeX source; word_guard.py checks the .docx.

When output_language is zh, the paper is Chinese. Produce final_paper/paper.zh.docx as the primary Word output instead of paper.docx — the .zh.docx suffix marks the language, not a translation:

pandoc paper_rewriting_output/final_paper/main.tex -o paper_rewriting_output/final_paper/paper.zh.docx --from latex --to docx --resource-path=paper_rewriting_output/final_paper --number-sections --citeproc --bibliography=paper_rewriting_output/final_paper/references.bib
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --fix-fonts

--citeproc --bibliography=... resolves \cite to linked [1] numbers in the .docx (matching the English command). Use it when citations come from a references.bib. If the paper instead carries a thebibliography block with \bibitem, drop --citeproc --bibliography=... — pandoc resolves \cite against \bibitem natively; either way the source must use \cite, never literal bracket text.

python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --markdown --output paper_rewriting_output/word_report.zh.md

If output_language is en, produce final_paper/paper.docx as the primary Word output. Do not produce or require final_paper/paper.zh.docx unless translation_package=zh is explicitly requested.

Gate (LaTeX):

python scripts/progress_check.py paper_rewriting_output --gate latex

Word guard (run only for the Word files requested by the config):

python scripts/word_guard.py paper_rewriting_output/final_paper/paper.docx --language en --fix-fonts
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.docx --language en --markdown --output paper_rewriting_output/word_report.md

When output_language=zh, run:

python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --fix-fonts
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --markdown --output paper_rewriting_output/word_report.zh.md

Gate (Word):

python scripts/progress_check.py paper_rewriting_output --gate word --require

Use --require so the gate checks Word even when config says none — the file should exist and be valid. If word_output is explicitly none, skip this gate.

Stage 9 — Submission Package (if requested)

If submission materials are requested, read references/publication-cycle.md, references/publication-target-profile.md, and references/submission.md. Research the current official author guide, create publication_target_profile.json, and verify it before producing files:

python scripts/publication_cycle.py profile-check \
  paper_rewriting_output/publication_cycle/targets/<target>/publication_target_profile.json \
  --markdown --write

Create submission_package_plan.json, transform and validate every required or applicable conditional item, obtain author-only confirmations, then assemble a new immutable bundle directory:

python scripts/publication_cycle.py assemble \
  paper_rewriting_output/publication_cycle/targets/<target>/publication_target_profile.json \
  paper_rewriting_output/publication_cycle/targets/<target>/submission_package_plan.json \
  paper_rewriting_output/publication_cycle/targets/<target>/bundles/<bundle-id> \
  --markdown

The package is upload-ready only when bundle_manifest.json status=READY, the ZIP exists, and its SHA-256 receipt matches. submission_check.py is a compatibility validator for legacy cover-letter/highlights packages, not the completeness authority for a real target.

Stage 10 — Translation Package (if applicable)

If output_language is en and translation_package is zh, read references/translate.md and produce the complete translation_zh/ package.

translation_zh/ is the translation audit/intermediate package, NOT the final user-facing Chinese document. The final Chinese deliverable is a single Word file under final_paper/. After translation_zh/full_paper_translation.zh.md is complete, generate the final Chinese Word document:

pandoc paper_rewriting_output/translation_zh/full_paper_translation.zh.md -o paper_rewriting_output/final_paper/paper.zh.docx
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --fix-fonts
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --markdown --output paper_rewriting_output/word_report.zh.md

Run python scripts/translate_guard.py paper_rewriting_output --markdown --write and require PASS. If pandoc is unavailable, write BLOCKED/FAIL in the translation report — do not silently skip the final Chinese Word document.

Gate:

python scripts/progress_check.py paper_rewriting_output --gate translation --require

Stage 11 — Review Response (if requested)

If the user requests review response / revision response, read references/publication-cycle.md and references/respond.md. Preserve and hash the decision sources, create an atomic review_round.json, confirm the author's position for each issue, and run:

python scripts/publication_cycle.py rebuttal-check \
  paper_rewriting_output/publication_cycle/revisions/<round-id>/review_round.json \
  --markdown --write
python scripts/publication_cycle.py rebuttal-render \
  paper_rewriting_output/publication_cycle/revisions/<round-id>/review_round.json \
  paper_rewriting_output/publication_cycle/revisions/<round-id>/rendered \
  --markdown

Minor revisions revalidate every readiness dimension and may mark a genuinely unaffected dimension not_affected. Major revisions and reject-and-resubmit rounds require all five dimensions to be re-run and passed. Package the revised manuscript, response letter, and target-required marked files through a new READY bundle. respond_check.py remains a legacy Markdown compatibility check.

Post-decision transfer branch: After rejection or when the user asks to change venue, read references/journal-transfer.md. Compare destinations against the user's must-haves and deal-breakers, obtain destination confirmation, create fresh origin/destination profiles and transfer_request.json, then run publication_cycle.py transfer-plan. Rebuild the destination format, all five narrative parts, and the entire delivery package from the canonical paper; never patch the old upload copy or silently accept a publisher transfer.

Stage 12 — Final Audit & Completion Hard Gate

Read references/audit.md. Before declaring the workflow complete, all checks below must pass. If any command fails or reports missing/content issues, the workflow is not complete; return to the failing upstream stage.

python scripts/artifact_check.py paper_rewriting_output --markdown --write
python scripts/citation_bank_check.py paper_rewriting_output/citation_support_bank.md --markdown --write
python scripts/scientific_evidence_check.py paper_rewriting_output --phase final --markdown --write
python scripts/publication_surface_check.py paper_rewriting_output --markdown --write
python scripts/visual_readiness_check.py paper_rewriting_output --markdown --write
python scripts/metadata_readiness_check.py paper_rewriting_output --markdown --write
python scripts/usage_ledger.py paper_rewriting_output --markdown --write
python scripts/progress_check.py paper_rewriting_output --gate final_audit
python scripts/integrity_audit.py paper_rewriting_output --markdown --write
python scripts/progress_check.py paper_rewriting_output --markdown --write

When word_output is not explicitly none, also run:

python scripts/word_guard.py paper_rewriting_output/final_paper/paper.docx --language en --fix-fonts
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.docx --language en --markdown --output paper_rewriting_output/word_report.md

When translation_package is zh or output_language is zh, also run:

python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --fix-fonts
python scripts/word_guard.py paper_rewriting_output/final_paper/paper.zh.docx --language zh --markdown --output paper_rewriting_output/word_report.zh.md

Before these commands, create submission_metadata.json per references/submission-metadata.md and maintain usage_ledger.jsonl per references/usage-telemetry.md. Completion may be declared only when artifact_check.py exits 0, final progress reports is_complete=true, no misplaced_artifacts are reported, integrity audit has no unresolved BLOCKER, and all five readiness dimensions are true: scientific_content_ready, visual_ready, citation_verified, metadata_ready, and artifact_portable. No green dimension offsets a red one. Word output remains required unless explicitly disabled. If pandoc is unavailable, write BLOCKED/FAIL in latex_report.md; never silently skip Word.

If a publication-cycle mode ran, its current authority must also be green: submission requires a READY bundle manifest and matching archive checksum; revision requires a PASS rebuttal check plus a new READY target bundle; transfer requires transfer_delta.json status=READY_TO_REBUILD, a completed destination rebuild, and a new READY destination bundle. Preparing local files never grants authority to press an external submit/transfer button.

Hard gate rules:

• artifact_check.md Status: FAIL or BLOCKED → workflow NOT complete; return to upstream stage.
• citation_bank_check.md Status: FAIL → citation bank unqualified; return to citation stage.
• Nested paper_rewriting_output/ inside paper_rewriting_output/ → misplaced; move contents up.
• Sibling final_paper/ outside paper_rewriting_output/ → misplaced; remove sibling copy.
• In strict mode, a generic or shallow writing_rationale_matrix.md remains a failure. Balanced mode does not require this matrix.

Chinese completion report rule: When the output language is Chinese (output_language=zh) or a Chinese translation package is requested (translation_package=zh), the final user-visible completion report must be written in Chinese. Use Chinese section titles and status labels. Prohibited: "PaperSpine Workflow Complete", "All stages passed", "Deliverables". Required minimum content: 工作流已完成、全部阶段已通过、交付文件清单. The final Chinese Word document is final_paper/paper.zh.docx; the translation_zh/ folder is an audit/intermediate package, not the final deliverable.

Loop Rule: If a gate fails, route back to that stage. Do not patch the final paper directly when the missing artifact should have been created earlier.

If a worker skill is unavailable, follow the reference playbook locally and produce the same artifacts.

Migration Note

See references/orchestrator-branch-map.md for stage ownership details.

Standard Artifacts

Write workflow artifacts under paper_rewriting_output/.

final_artifact_manifest.md must label each artifact with its source category:

• required — always produced
• pro-extra — produced only in pro tier (additional analysis depth)
• optional-translation — produced when translation package is requested
• optional-submission — produced when submission materials are requested
• optional-review-response — produced when review response workflow runs
• optional-transfer — produced when a rejected or redirected paper is rebuilt for another target

Common required artifacts: paper_spine_config.json, paper_spine_config.md, source_map.md, reference_materials/source_index.md, research_dossier.md, exemplar_learning_dossier.md, style_profile.md, sota_gap_map.md, contribution_options_after_research.md, motivation_options_after_research.md, citation_support_bank.md, confirmed_contribution.md, confirmed_motivation.md, section_blueprints.md, structured_review.md; strict mode also requires writing_rationale_matrix.md and reviewer_audit.md; plus results_validation.md and scientific_evidence_ledger.json for journal, conference, and competition scenes; plus submission_metadata.json, usage_ledger.jsonl, and the visual/publication-surface audit receipts before final completion. Figure-active work also requires figure_requests.json and figure_story_check.md.

Rewrite existing: original_logic_map.md, evidence_bank.md, rewrite_matrix.md, logic_transfer_audit.md, revised manuscript.

Build from materials: source_inventory.md, evidence_bank.md, figure_asset_map.md, claim_register.md, manuscript draft.

Final artifacts: latex_report.md, final_artifact_manifest.md, final_paper/main.tex, final_paper/paper.pdf (when TeX available), final_paper/paper.docx + word_report.md (standard; skip only if word_output is explicitly none), final_paper/paper.zh.docx + word_report.zh.md (when output_language=zh or translation_package=zh; translation_zh/ is the audit/intermediate package, NOT the final Chinese deliverable), publication_cycle/targets/<target>/publication_target_profile.json, submission_package_plan.json, and an immutable bundles/<bundle-id>/ with bundle_manifest.json, submission_bundle.zip, and submission_bundle.sha256 (when submission materials are requested and READY).

Review-cycle artifacts: publication_cycle/revisions/<round-id>/review_round.json, rebuttal_check.md, response_matrix.md, response_letter.md, and revision_change_log.md; the revised files then enter a new target bundle.

Transfer artifacts: publication_cycle/transfers/<id>/transfer_request.json and transfer_delta.json, followed by a newly rendered destination manuscript and target-specific READY bundle.

Writing Rationale Matrix (Strict / Optional Trace)

Use writing_rationale_matrix.md before final writing in strict mode or when the user requests a paragraph-level rationale trace. It is not required by the balanced default:

When used, the first data row should justify the whole-work framework. Subsequent rows split the document into the smallest useful writing units. Contribution is the governing column; motivation explains significance but cannot substitute for a claim ID or enlarge its boundary. Do not create rows that merely paraphrase the template; prefer a shorter plan containing genuine decisions.

Command-Line UI

Claude Code and Codex do not guarantee a native graphical picker for skills. The supported UI is the bundled terminal wizard. When configuration is missing, read references/intake.md to launch the intake UI. In Claude Code, /paperspine must launch the intake UI automatically.