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CLAUDE.md — index-template (Claude Code)

This is the Claude Code pointer. The full agent contract is in AGENTS.md — read it. This file only adds Claude-specific notes.

What this repo is

A knowledge pack (like BAIT) that teaches an agent to build a sdmTMB survey index for a species and generates a new project folder for it. It is installed once per machine; its skills live in ~/.claude/skills/ as index-*. It is public — never commit data or private paths here. See the privacy section of AGENTS.md.

Where things are

  • Skills — skills/index-*/SKILL.md. Installed globally by skills/index-install.
  • Shared knowledge — knowledge/*.md (the method, filtering, sdmTMB, helpers, packages, project structure, rendering).
  • Project skeleton — project-template/, copied and stamped by scaffold.R for each new species project.
  • Worked example — examples/redfish/.

Claude-specific notes

  • Project memory, not local memory. When working inside a generated project, use that project's memory/ folder as your project memory (read memory/MEMORY.md first, write new memory files there). Do not use ~/.claude/projects/.../memory/ for project facts — that folder is only for user-level preferences/identity.
  • Skills — when the user types /index-... or asks to build/validate/report an index, invoke the matching skill. When they ask for Biotic data access, defer to BAIT's biotic-* skills.
  • Plan mode — after the questionnaire in index-new-project, use plan mode to confirm the approach before scaffolding and rendering.
  • Code review before render — Quarto renders are slow; run /code-review on changed chunks and fix issues before starting a render. See knowledge/rendering.md.

For everything else, see AGENTS.md.