init

name	init
description	Fills all [FILL:] placeholders across the template to initialize a new research project. Use when setting up a freshly cloned project.
disable-model-invocation	true
allowed-tools	Bash, Read, Write, Edit, Glob, Grep

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:

   grep -rn "\[FILL:" --include="*.md" --include="*.qmd" --include="*.toml" --include="*.tex" --include="*.yml" .
   

   Report how many placeholders exist and in which files.

2. 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)

3. 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

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

   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...").

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

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