Setup

Local setup

Requirements: git, Claude Code CLI, Codex, and/or Cursor.

git clone https://github.com/Morrison-Lab/ai-config.git ~/ai-config
bash ~/ai-config/bootstrap.sh

bootstrap.sh symlinks Claude assets into ~/.claude/, generated Codex wrappers into ${CODEX_HOME:-$HOME/.codex}/skills, Cursor user rules into ${CURSOR_HOME:-$HOME/.cursor}/rules when no Cursor plugin is already serving them, and — when no Cursor plugin or Claude skill install is already serving the catalog — Cursor skills into ~/.cursor/skills/. Run it again any time you add a new top-level dir to the repo.

Verify the install

ls -l ~/.claude/skills ~/.claude/commands ~/.codex/skills
# ~/.cursor/rules is linked only when no Cursor plugin is already serving those rules
scripts/inventory.sh                         # live counts of skills/wrappers/commands/docs

In a Claude Code session, type / and confirm skills appear (e.g. /ardi, /scout-peers).

In Codex, the wrappers appear as skills from ${CODEX_HOME:-$HOME/.codex}/skills. Each wrapper reads the matching canonical workflow from skills/<name>/SKILL.md and adapts Claude-specific metadata/tools to Codex.

In Cursor, open Customize -> Rules and confirm the cursor-rules/ files appear as user rules (from the plugin, or from ~/.cursor/rules/ when no plugin is installed). Skills appear under Customize -> Skills from the plugin, from ~/.claude/skills, or from ~/.cursor/skills/.

Web (cloud) sessions — this repo

In cloud sessions (claude.ai or remote environments), bootstrap.sh can’t run at startup because the repo isn’t on disk yet. The committed SessionStart hook (.claude/settings.json → .claude/hooks/session-start.sh) runs bootstrap.sh once the repo is checked out, symlinking skills/ and commands/ into ~/.claude/. The hook is a no-op outside remote sessions (CLAUDE_CODE_REMOTE) and is idempotent.

The hook also installs Julia (via juliaup) on first start, if allowed by the environment’s network policy. See docs/julia-setup.md.

Plugin marketplace — other repos

To load these skills when a different repo is open in a cloud session, add this to that repo’s .claude/settings.json:

{
  "extraKnownMarketplaces": {
    "Morrison-Lab": {
      "source": { "source": "github", "repo": "Morrison-Lab/ai-config" }
    }
  },
  "enabledPlugins": {
    "ai-config@Morrison-Lab": true
  }
}

Claude Code installs the plugin at session start. Skills are namespaced: /ai-config:ardi, /ai-config:reprexes, etc.

Or try it interactively in any Claude Code session:

/plugin marketplace add Morrison-Lab/ai-config
/plugin install ai-config@Morrison-Lab
WarningPick one install route

The plugin install and the bootstrap.sh symlink install are alternatives, not complements: both serve the same corpus, so running both lists every skill twice (bare /ardi plus prefixed /ai-config:ardi) and blows the skill-listing context budget (ai-config#1409). On a machine that ran bootstrap.sh, leave the plugin disabled — including a consumer repo’s checked-in enabledPlugins block, which you opt out of with "ai-config@Morrison-Lab": false in .claude/settings.local.json. Not ~/.claude/settings.json: the user scope is the lowest of Claude Code’s five, so a false there loses to the repo’s checked-in true (settings docs). Likewise enable the plugin from at most one marketplace: Morrison-Lab/ai-config and d-morrison/ai-config publish the same plugin, so a second entry is a no-op collision. bootstrap.sh warns about both cases via scripts/check-plugin-overlap.py.

@claude bot on PRs

The bot that runs claude-code-action on this repo’s PRs reads skills from .claude/skills/. The .claude/skills → ../skills symlink is committed to main, so restoreConfigFromBase always restores it — even on PR branches. Comment @claude ardi (or any skill name) on a PR and the bot can run it.

Deconflicting parallel local sessions

When several AI sessions share one local checkout, they can clobber each other. The session-lock skill (alias deconflict-sessions) keeps a machine-local registry of active sessions under .git/ai-sessions/. Sessions can refuse to share a working tree and isolate into a git worktree. See docs/local-session-deconfliction.md.

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