Manuscript Setup

Manuscript Setup

Scaffold a new or augment an existing Quarto-based manuscript project for journal submission.

When to Use

Use this skill when:

• Starting a new manuscript project from scratch
• Adding quartopress build pipeline to an existing project
• Converting an existing draft into a structured Quarto project
• Setting up table/figure generation in a project that already has .qmd files

New vs. Existing Projects

New project: quartopress-init ./my-manuscript --title "My Study" Creates the full directory structure, all section templates, build scripts, and bibliography files.

Existing project: quartopress-init . Detects what's already present (.qmd sections, .bib files, build scripts, table builder) and adds only what's missing. Never overwrites existing files unless --force is used.

Force mode: quartopress-init . --force Overwrites all files with fresh templates. Use when you want to reset to defaults.

Project Structure

The scaffold creates:

manuscript-project/
├── manuscript/
│   ├── manuscript.qmd              # Master Quarto file (includes all sections)
│   ├── _sections/
│   │   ├── _title_page.qmd         # Title, authors, affiliations
│   │   ├── _abstract.qmd           # Structured abstract
│   │   ├── _introduction.qmd       # Background, gap, objectives
│   │   ├── _methods.qmd            # Study design, measures, analysis
│   │   ├── _results.qmd            # Primary and secondary outcomes
│   │   └── _discussion.qmd         # Interpretation, limitations, conclusions
│   ├── _templates/
│   │   └── journal-reference.docx  # Journal Word template (controls formatting)
│   ├── references.bib              # BibTeX bibliography
│   └── citation-style.csl          # Citation style (AMA, Vancouver, etc.)
├── data/
│   ├── tables/                     # CSV source files for tables
│   └── figures/                    # Data files for figure generation
├── scripts/
│   ├── prs_table_builder.py        # Reusable table generation module
│   ├── build_tables.py             # Declarative table definitions
│   └── build_upload.py             # Master build script
├── output/                         # Generated submission files
│   ├── Manuscript.docx
│   ├── Table 1.docx
│   ├── Figure 1.tiff
│   └── ...
└── review/                         # Reviewer feedback and responses
    ├── reviewer_comments.md
    ├── response_to_reviewers.md
    └── compliance_checklist.md

Setup Steps

1. Create the project directory

mkdir -p manuscript-project/{manuscript/_sections,manuscript/_templates,data/tables,data/figures,scripts,output,review}

2. Copy core modules

Copy prs_table_builder.py from the plugin's scripts/ directory into scripts/.

3. Create the master Quarto file

Use the template from ${CLAUDE_PLUGIN_ROOT}/templates/manuscript_unified.qmd. Configure:

• reference-doc pointing to your journal's Word template
• bibliography pointing to your .bib file
• csl pointing to your citation style

4. Create section files

Each section is a separate .qmd file. Start with the templates from ${CLAUDE_PLUGIN_ROOT}/templates/_sections/.

5. Set up the build pipeline

Copy build_tables.py and build_upload.py templates from the plugin. Customize:

• Table definitions (from your CSV data)
• Figure copy paths
• Cross-reference map (table/figure label to number)
• Figure legends and SDC legends

6. Configure for your journal

Update word limits, abstract structure, figure requirements, and reference format based on your target journal's author guidelines.

Journal Configurations

Journal	Word Limit	Abstract	Figures	Tables	Reference Style
PRS	3,000 (+500 ext)	250, structured	300 DPI TIFF	Separate .docx	AMA
JPRAS	4,000	250, structured	300 DPI TIFF/EPS	Separate .docx	Vancouver
Ann Plast Surg	3,000	200, unstructured	300 DPI TIFF	Embedded	AMA

Key Principles

1. Sections as separate files — enables parallel editing and targeted AI review
2. Tables from data — CSV is the source of truth; .docx is generated output
3. Figures from code — data-driven, reproducible, never hardcoded
4. One build command — uv run python scripts/build_upload.py generates everything
5. Cross-references resolved at build time — Quarto handles citations; build script handles table/figure numbering