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, or check for updates, read `references/update.md` and execute without starting the full writing workflow. ## Command Routing | Trigger | Read | |---|---| | Default / full workflow | This file (Non-Negotiable Route below) | | `resume` / `continue` / "continue from" | `references/resume.md` | | `update` / "check for updates" | `references/update.md` | | `submission` / "submission materials" | `references/submission.md` | | `audit` | `references/audit.md` | | `translate` | `references/translate.md` | | `humanize` | `references/humanize.md` | | `respond` / `response letter` / `reviewer comments` | `references/respond.md` | For fine-grained stage execution, the orchestrator reads the playbook for each stage from `references/` rather than requiring a separate skill invocation: | Stage | Playbook | |---|---| | Intake / config | `references/intake.md` | | Resume / checkpoint | `references/resume.md` | | Research | `references/research.md` | | Citation | `references/citation.md` | | Rewrite | `references/rewrite.md` | | Build | `references/build.md` | | Humanize | `references/humanize.md` | | LaTeX | `references/latex.md` | | Translate | `references/translate.md` | | Respond | `references/respond.md` | | Audit | `references/audit.md` | 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 strong examples first, force a user-confirmed motivation, design the paper row by row, and only then write or rebuild the manuscript. 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. ## 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 Stage 12 Final Audit hard gate runs all three checks; do not declare the work complete while any of them fails. ## 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: | Field | Allowed Values | |---|---| | `workflow` | `rewrite_existing`, `build_from_materials` | | `scene` | `journal`, `conference`, `report_review`, `competition` | | `tier` | `flash`, `pro` | | `output_language` | `en`, `zh` | | `target_name` | free text | | `materials_dir` | path or empty | | `draft_path` | path or empty | | `user_motivation` | free text or empty | | `official_urls` | list | | `special_requirements` | list | | `word_output` | `none`, `docx` | | `translation_package` | `none`, `zh` | | `reference_mode` | `local_first`, `specified_paths`, `web` | | `reference_paths` | list of local reference folders/files; default `["."]` | | `citation_target_count` | integer; default `20` | | `humanize_tier` | `none`, `light`, `medium`, `heavy` | ## 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:** ```bash 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`, `motivation_options_after_research.md`. **Gate:** ```bash 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`. Generate at least `citation_target_count * 3` candidates (default: 60). ~80% recent. Include Source Channel for every row. **Gate:** ```bash python scripts/progress_check.py paper_rewriting_output --gate citation ``` If FAILED: return to citation. The bank must exist with sufficient candidates. ### Stage 4 — Motivation Confirmation Stop for user confirmation of the controlling motivation. Write `confirmed_motivation.md` only after the user chooses. This stage is BLOCKED (not just pending) until the user confirms. Present `motivation_options_after_research.md` and wait. Do not auto-select. **Gate:** ```bash python scripts/progress_check.py paper_rewriting_output --gate motivation_confirmation ``` If FAILED/BLOCKED: stop and wait for user. Do not proceed with an unconfirmed motivation. ### 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 must create `section_blueprints.md` and `writing_rationale_matrix.md` before drafting. **Gate:** ```bash python scripts/progress_check.py paper_rewriting_output --gate planning ``` If FAILED: return to the writing stage. Blueprints and rationale matrix are mandatory — a paper without a documented design is not a PaperSpine paper. ### Stage 7 — Integrity Audit Run integrity audit before LaTeX assembly: ```bash python scripts/integrity_audit.py paper_rewriting_output --markdown --write ``` Review BLOCKER findings. Return to the relevant stage for any BLOCKED dimension. Do not proceed to LaTeX with unresolved BLOCKERs. **Gate:** ```bash python scripts/progress_check.py paper_rewriting_output --gate integrity_audit ``` If FAILED: run the audit, fix BLOCKERs, re-run until 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`. **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: ```bash 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. ```bash 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):** ```bash python scripts/progress_check.py paper_rewriting_output --gate latex ``` **Word guard (run only for the Word files requested by the config):** ```bash 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: ```bash 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):** ```bash 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/submission.md`, create `submission_package/`, and run: ```bash python scripts/submission_check.py paper_rewriting_output/submission_package --fix-fonts --markdown --write ```