Research Setup Wizard

Walk the user through setup using AskUserQuestion menus wherever possible. Collect all answers, then write config files in one pass.

This skill is the only entry point that seeds project config (references/domain-profile.md, CLAUDE.md). The plugin does not scaffold anything on session start.

Read ${CLAUDE_PLUGIN_ROOT}/skills/research-setup/references/workflow-overview.md before explaining the workflow or next-step sequence.

Step 0: Bootstrap & Check Existing Config

Seed missing config files into the project, then read what's there.

1. Seed references/domain-profile.md if absent. Run via Bash (idempotent — only copies when missing):

   if [ ! -f ./references/domain-profile.md ]; then
     mkdir -p ./references
     cp "${CLAUDE_PLUGIN_ROOT}/references/domain-profile.md" ./references/domain-profile.md
   fi

2. Seed CLAUDE.md if absent. Use Glob to check. If missing, Write this placeholder:

   # [YOUR PROJECT NAME]
   
   **Author:** [YOUR NAME]
   **Institution:** [YOUR INSTITUTION]

3. Now Read CLAUDE.md and references/domain-profile.md silently. If either has real content (not placeholders), tell the user what's already configured and offer to confirm or update each section.

Step 1: Field

AskUserQuestion — 1 question:

1. Field (single select, header: "Field"): "What is your field or subfield?" — Options: "Political Science", "Economics", "Sociology", "Public Health". User selects Other for unlisted fields.

Store field for customizing later steps.

Step 2: Identity & Project Title

Ask conversationally (not via AskUserQuestion):

1. "What is your name (for paper authorship)? You can skip this for now."
2. "What is your institution? (This helps customize figure color palettes and LaTeX title pages.)"
3. "Do you have a working title for your current project? Fine to skip if you're still exploring."

Wait for the user's response before moving to Step 3.

Step 3: Journals

AskUserQuestion — 2 multi-select questions based on the user's field:

1. Top journals (multiSelect, header: "Top journals"): "Select your top journals (pick all that apply):" — Offer the 4 most prestigious journals for the user's selected field. Use your knowledge of the field's top venues.
2. Secondary journals (multiSelect, header: "Secondary"): "Select secondary or subfield journals:" — Offer 4 secondary/subfield journals appropriate to the user's field.

User can multi-select presets and add custom journals via Other.

Step 4: Datasets

AskUserQuestion — 2 multi-select questions based on the user's field:

1. Common datasets (multiSelect, header: "Datasets"): "Which datasets do you commonly use?" — Offer the 4 most-used datasets for the user's field. Use your knowledge of field-standard data sources.
2. Additional sources (multiSelect, header: "More data"): "Any additional data sources?" — Offer 4 cross-disciplinary sources: World Bank Open Data, IPUMS, Bureau of Labor Statistics, Census Bureau.

Step 5: Researchers & Colors

AskUserQuestion — 2 questions at once:

1. Researchers (single select, header: "Researchers"): "Add key researchers for targeted literature searches?" — Options: "Skip for now" / "Add researchers".
2. Colors (single select, header: "Colors"): "Which color palette should R figures use?" — If the institution is well-known, offer its official brand colors as the recommended option with a preview showing the hex codes. Otherwise offer: "Custom colors" / "Skip for now".

If the user chose "Add researchers", ask conversationally for names, institutions, and Google Scholar URLs. Do NOT guess researcher names.

If the user chose "Custom colors", ask conversationally for primary and secondary hex codes.

Step 6: Write Config Files

references/domain-profile.md

Read the existing file and update each section with the user's answers. Preserve the file's existing structure and comments. Only replace sections the user answered; leave unanswered sections unchanged. Add an "Institutional Colors" section at the end if one doesn't exist, with the user's hex codes (or defaults #012169 / #f2a900 if skipped).

IMPORTANT: Do NOT write to ${CLAUDE_PLUGIN_ROOT}/rules/r-code-conventions.md. Colors live in references/domain-profile.md only.

CLAUDE.md

Update the project header placeholders:

• [YOUR PROJECT NAME] → user's project title (or leave placeholder if skipped)
• [YOUR NAME] → user's name (or leave placeholder if skipped)
• [YOUR INSTITUTION] → user's institution

Step 7: Confirm

Setup complete:
- references/domain-profile.md — field, [N] journals, [N] datasets[, N researchers][, colors]
- CLAUDE.md — project name and institution

Update anytime: references/domain-profile.md
Next step: /new-project

Note any skipped sections and where to add them later.