Initialize Project

Fill in all [FILL:] placeholders across the template to set up a new research project.

Steps

1. Scan all tracked files for [FILL: patterns and group them by file:

bash grep -rn "\[FILL:" --include="*.md" --include="*.qmd" --include="*.toml" --include="*.tex" --include="*.yml" . Report how many placeholders exist and in which files.

1. Ask the user for project information:

• Project title (used in index.qmd, README.md, CLAUDE.md, pyproject.toml)
• Subtitle (optional, for index.qmd)
• Authors — for each author:
• Name, affiliation (university, city, country), ORCID, email
• Whether they are the corresponding author
• Abstract (for index.qmd)
• Keywords (for index.qmd)
• Project stage (for CLAUDE.md: Idea / Data collection / Analysis / Writing / Revision)
• Data source description (for CLAUDE.md and README.md)
• Repository URL (for README.md)
• Project slug (for pyproject.toml name field, e.g., regional-gdp-study)

1. Apply the values to each file:

• index.qmd — title, subtitle, authors (full YAML array with affiliations/ORCID/email), abstract, keywords
• README.md — project title, description paragraph, data section, repository URL, Quick Start clone URL
• CLAUDE.md — Project Context table: title, authors, stage, data source
• pyproject.toml — name, description, authors
• _quarto.yml — no [FILL:] placeholders by default, but verify
• templates/chadManuscript/manuscript.tex — author names and keywords

1. After applying all values, re-scan for remaining [FILL:] placeholders:

bash grep -rn "\[FILL:" --include="*.md" --include="*.qmd" --include="*.toml" --include="*.tex" --include="*.yml" . Report how many remain and where (some are expected in section bodies like "Describe the data...").

1. Run bash scripts/render.sh to regenerate latex/index.tex with the real content.

1. Report a summary: files updated, placeholders filled, placeholders remaining, render status.