paper-covert

name	paper-covert
description	Converts the final Markdown manuscript from `paper-draft` / `paper-review-loop` into a submission package for the target venue — modular LaTeX (one file per section), compiled PDF, and Word `.docx`. Venue is read from `output/PAPER_PLAN.md` (or argument) and routed through a small YAML profile. Does not rewrite prose, score, or invent citations.
argument-hint	["venue-or-manuscript-path"]
allowed-tools	Bash(*), Read, Write, Edit, Grep, Glob

Skill: paper-covert

Convert the final manuscript in output/manuscript/ into a submission package for: $ARGUMENTS

Naming: the pipeline in paper-writing-pipeline references this as /paper-convert. Folder name is paper-covert per invocation; they resolve to the same skill.

---

Constants

• SRC — first existing of: output/manuscript/MANUSCRIPT_REVISED.md → output/manuscript/MANUSCRIPT_DRAFT.md → concatenated sections_revised/*.md → concatenated sections/*.md.
• SECTIONS_SRC — output/manuscript/sections_revised/ if present, else sections/.
• PLAN = output/PAPER_PLAN.md — for title, keywords, venue, figure/table plan, declarations.
• OUT = output/submission/
• VENUE — argument venue:<name> → PAPER_PLAN.md §0/§2 → research_contract.md → IJGIS.
• PROFILE — ./profiles/<venue>.yaml, else ./profiles/generic.yaml.

Inline override: /paper-covert — venue: ISPRS, mode: latex. Modes: all (default), latex, pdf, docx.

---

Inputs

Primary:

• SRC (Markdown manuscript)
• SECTIONS_SRC/*.md
• PLAN

Supporting (read when present):

• output/manuscript/CLAIM_RISK_REPORT.md, COVERAGE_GAPS.md, CITATION_GAPS.md — surface unresolved items into the manifest, do not fix them.
• output/figures/FIGURE_MANIFEST.md, output/figures/FIGURE_CAPTIONS.md, output/figures/
• memory/paper-cache/*.json, local references.bib
• data/DATA_MANIFEST.md, research_contract.md
• ./profiles/<venue>.yaml

---

Outputs

output/submission/
├── SUBMISSION_MANIFEST.md      # source, venue, files, readiness, unresolved items
├── latex/
│   ├── main.tex                # lean entry: \input's only
│   ├── preamble.tex            # packages + placeholder env
│   ├── metadata.tex            # title, authors, keywords, highlights
│   ├── references.bib          # copied or synthesized; else stub
│   ├── build.sh                # latexmk → pdflatex fallback
│   ├── sections/
│   │   ├── 01_abstract.tex
│   │   ├── 02_introduction.tex
│   │   ├── 03_related_work.tex
│   │   ├── 04_data.tex
│   │   ├── 05_methodology.tex
│   │   ├── 06_experiments.tex
│   │   ├── 07_results.tex
│   │   ├── 08_discussion.tex
│   │   ├── 09_limitations.tex
│   │   ├── 10_conclusion.tex
│   │   ├── 11_declarations.tex
│   │   └── appendix_*.tex
│   └── figures/                # copied from output/figures/ per FIGURE_MANIFEST
├── pdf/MANUSCRIPT_SUBMISSION_READY.pdf
└── docx/MANUSCRIPT_SUBMISSION_READY.docx

Filenames are stable; overwrite in place. Two-digit zero-padded section prefixes match paper-draft.

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Workflow

1. Resolve source and venue

Pick SRC by priority above. Read PLAN for title, keywords, venue, declarations, figure/table plan. Load PROFILE. Record the source path, venue, and profile choice at the top of SUBMISSION_MANIFEST.md.

2. Build the LaTeX tree

• Write main.tex, preamble.tex, metadata.tex from ./templates/, filling in profile fields (documentclass, class_options, bib_style, bib_engine) and manuscript metadata (title, keywords, highlights when the venue requires them).
• For each section in SECTIONS_SRC/, write one .tex file under latex/sections/ using these conversion rules:
  • #/##/### → \section/\subsection/\subsubsection with a \label{sec:...}.
  • Markdown emphasis, lists, block quotes, inline/display math → LaTeX equivalents.
  • Markdown tables → booktabs tabular; tables ≥ 15 rows extracted to tables/.
  • Images ![cap](figures/X.png) → figure env with \includegraphics, \caption, \label{fig:X}.
  • Citations: \cite{key} kept as-is when resolvable in references.bib; [CITE: topic] rendered via a visible \citeplaceholder{topic} macro and logged in the manifest.
  • [PLACEHOLDER — …] blocks wrapped in a visible placeholder environment so they show in the PDF.
• Copy figures listed in FIGURE_MANIFEST.md into latex/figures/. Do not reference figures not in the manifest.

Section file mapping adapts to the manuscript's actual section list; PLAN §19 is authoritative when it differs from the default 01–11 layout. Appendices use appendix_<letter>.tex.

3. Wire the bibliography

• If a .bib exists under output/manuscript/ or repo root → copy to latex/references.bib.
• Else synthesize from memory/paper-cache/*.json — copy only entries whose keys appear in the manuscript; never invent.
• Use bib_style and bib_engine from the profile. Unresolved [CITE: …] or missing keys → list in the manifest's Bibliography gaps section; do not fabricate.

4. Build the PDF

Write build.sh from ./templates/build_script_template.sh. Run it (latexmk -pdf; fallback to pdflatex + bibtex + pdflatex ×2). Copy main.pdf to pdf/MANUSCRIPT_SUBMISSION_READY.pdf. On failure, keep the LaTeX tree intact and record the first error + likely cause in the manifest under Build.

5. Export the DOCX

Prefer pandoc latex/main.tex -o docx/MANUSCRIPT_SUBMISSION_READY.docx --citeproc --bibliography=latex/references.bib. If Pandoc rejects venue LaTeX, fall back to pandoc on the source Markdown (concatenated SECTIONS_SRC/*.md). If Pandoc is unavailable, record docx: blocked in the manifest.

6. Write the manifest

Write SUBMISSION_MANIFEST.md from ./templates/SUBMISSION_MANIFEST_TEMPLATE.md:

• source manuscript path + readiness (reviewed / revised / draft-only)
• venue + profile (flag fallback generic explicitly)
• files generated with paths
• Bibliography gaps (unresolved citations) — carried from CITATION_GAPS.md plus anything new.
• Asset gaps — figures referenced but missing from the manifest; figures marked Needs revision.
• Content gaps — [PLACEHOLDER …] blocks remaining in the LaTeX.
• Build — PDF engine, pass/fail, warning counts; DOCX pathway, pass/fail.
• Readiness — honest per-format statement. Do not mark "submission-ready" while any gap above is open or a build failed.

Append one line to output/PROJ_NOTES.md:

YYYY-MM-DD paper-covert venue=<V> source=<revised|draft> pdf=<ok|fail> docx=<ok|fail> gaps=<K>

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Decision rules

• Venue structure: PROFILE defaults → PLAN §19 overrides. Log the final structure in the manifest.
• No publisher class bundled: use article + the profile's bib style; record in the manifest that a publisher re-wrap is needed at submission time. Never claim the output is an official publisher template.
• Incomplete manuscript: still produce the package; placeholders stay visible; readiness is partial.
• Mode restriction: mode:latex stops after step 3; mode:pdf skips DOCX; mode:docx still needs LaTeX for the Pandoc path unless Markdown→DOCX is forced.

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Guardrails

Do not:

• rewrite, soften, or restructure prose — that is paper-review-loop.
• invent citations, bibliographic entries, figure files, or publisher-private rules.
• reference figures not listed in FIGURE_MANIFEST.md.
• silently drop content when a format conversion can't handle it — log it.
• label the package "submission-ready" with open gaps or a failed build.
• modify output/manuscript/. This skill is read-only on it.

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Supporting files

Under this skill:

• templates/main_template.tex, preamble_template.tex, metadata_template.tex, section_template.tex, build_script_template.sh, SUBMISSION_MANIFEST_TEMPLATE.md, CONVERSION_CHECKLIST.md, VENUE_ROUTING_README.md, BIBLIOGRAPHY_GAP_CHECKLIST.md.
• profiles/: generic.yaml, ijgis.yaml, isprs_jprs.yaml, rse.yaml, tgis.yaml, aag_annals.yaml, ieee_tgrs.yaml. Each profile declares documentclass, class_options, bib_style, bib_engine, word/abstract/figure limits, highlights requirement, and a note on publisher-class availability.

Composing with other skills

/paper-draft → /paper-review-loop → /paper-covert → /submit-check

paper-covert packages; submit-check validates venue compliance. They do not overlap.