Repository Initialization

Scaffold a new or existing repository with standard project infrastructure.

Related skills:

• just-pro - Build system patterns and templates
• mise - Tool version management
• output-compression - CLI output compression (RTK + tokf)
• Timbers (timbers init) - Development reasoning ledger
• go-pro, rust-pro, typescript-pro, python-pro - Language-specific setup

Execution Modes

This skill supports two modes. Prefer molecule mode when beads is available.

Molecule Mode (Preferred)

Use beads molecules for tracked, closeable tasks. Each step becomes an issue you can close as you complete it.

Prerequisites: beads installed (bd --version works)

Steps:

1. Find the dm-work plugin install path:

   jq -r '.plugins["dm-work@dark-matter-marketplace"][0].installPath' ~/.claude/plugins/installed_plugins.json
   

2. Wisp the formula (ephemeral, no git pollution):

   bd mol wisp <install-path>/skills/repo-init/references/repo-init.formula.json \
     --var lang=<language> --var name=<project-name> --var type=<project-type>
   

3. Work through tasks:

   bd ready              # See next task
   # ... do the work ...
   bd close <step-id>    # Mark complete
   

4. Clean up when done:

   bd mol burn <wisp-id>
   

Variables:

Variable	Required	Default	Values
lang	Yes	-	go, rust, typescript, python
name	Yes	-	Project name
type	No	cli	cli, lib, web, api

---

Manual Mode (Fallback)

Use when beads is not installed or for quick setups without tracking.

Follow the steps below in order. Steps 3-6 can run in parallel after git-init.

---

Step 1: Gather Context

Before scaffolding, clarify:

1. Project language(s): Go, Rust, TypeScript, Python, or multi-language?
2. Project type: Library, CLI, web app, API, monorepo?
3. Existing files: Is this a fresh repo or adding to existing code?

Use AskUserQuestion if unclear from context.

---

Step 2: Git Setup

# Initialize git if needed
git init

.gitignore Templates

Copy from the appropriate language skill's references/gitignore:

Language	Source
Go	go-pro/references/gitignore
Rust	rust-pro/references/gitignore
TypeScript	typescript-pro/references/gitignore
Python	python-pro/references/gitignore

For multi-language repos: Start with the primary language's gitignore, then merge patterns from others.

Minimal fallback (if language skill unavailable):

# Environment
.env
.env.local
.env.*.local
.envrc

# OS
.DS_Store
Thumbs.db

# IDE
.idea/
.vscode/

# Build (customize per language)
dist/
build/
target/
node_modules/
__pycache__/

.claudeignore

Every repo should have a .claudeignore file. Claude Code indexes everything it can see — without ignore patterns, it reads build artifacts, generated files, and large binaries, wasting massive token budget. This is the single highest-impact CC optimization.

Universal base (all projects):

# Secrets — never leak into CC context
.env
.env.*
.envrc
secrets/
*.pem
*.key
*.p12

# Lock files (large, no signal)
pnpm-lock.yaml
package-lock.json
yarn.lock
bun.lockb
Cargo.lock
go.sum
Gemfile.lock
poetry.lock

# Source maps
*.map

# Binary assets (images, fonts)
*.png
*.jpg
*.jpeg
*.gif
*.ico
*.svg
*.woff
*.woff2
*.ttf
*.eot

# Logs and OS
*.log
logs/
.DS_Store

# Agent working dirs
.worktrees/
history/

Add language-specific patterns:

Language	Patterns
TypeScript/Node	node_modules/, dist/, build/, .next/, coverage/, *.tsbuildinfo, .turbo/, .cache/
Python	__pycache__/, .venv/, venv/, *.pyc, .mypy_cache/, .pytest_cache/, dist/, build/, *.egg-info/
Go	vendor/, bin/
Rust	target/
AI/ML	output/, models/, *.safetensors, *.ckpt, *.pt, *.bin, checkpoints/

For multi-language repos: Combine all relevant language patterns.

---

Step 3: AGENTS.md

Copy the AGENTS.md template from this skill's references/AGENTS.md to the project root, then create a symlink so Claude Code discovers it automatically:

cp "${CLAUDE_PLUGIN_ROOT}/skills/repo-init/references/AGENTS.md" ./AGENTS.md
ln -s AGENTS.md CLAUDE.md

AGENTS.md is the canonical file; CLAUDE.md is a symlink so Claude Code discovers it automatically. Verify after creation: readlink CLAUDE.md should print AGENTS.md, and test -e CLAUDE.md should succeed (catches dangling symlinks).

Customize the template for the specific project (update project description, add project-specific conventions).

Symlink fallback (Windows or FS without symlink support): if ln -s fails or symlinks aren't usable, use the stub pattern instead — keep AGENTS.md canonical and make CLAUDE.md a one-line stub:

echo "See @AGENTS.md" > CLAUDE.md

Claude Code's @path import resolves the reference at session start. Higher maintenance than a symlink (two real files) but works everywhere.

CLAUDE.local.md (personal project prefs)

Create CLAUDE.local.md for personal preferences that shouldn't be committed (it's auto-added to .gitignore):

cat > CLAUDE.local.md << 'EOF'
# Personal Project Preferences
# This file is gitignored — safe for local paths, sandbox URLs, etc.

# For worktrees: import shared personal prefs so all worktrees stay in sync
# @~/.claude/my-project-instructions.md
EOF

Use this for sandbox URLs, test data paths, local tool overrides, and other per-developer settings.

Modular rules (monorepos)

For monorepos or projects with distinct subsystems, use .claude/rules/ instead of a single large CLAUDE.md:

.claude/
├── CLAUDE.md              # Core project instructions
└── rules/
    ├── go-backend.md      # Go-specific rules
    ├── ts-frontend.md     # TypeScript-specific rules
    └── api-design.md      # API conventions

All .md files in .claude/rules/ are auto-loaded. Rules can be path-scoped via YAML frontmatter to only activate when Claude touches matching files:

---
paths:
  - "packages/api/**/*.go"
---

# API Backend Rules
- All handlers return structured errors
- Use slog for logging, never fmt.Print

Skip this for single-language repos — a single CLAUDE.md is simpler.

---

Step 4: Justfile Skeleton

# Project Build System
# Usage: just --list

default:
    @just --list

# First-time setup
setup:
    mise trust
    mise install
    @echo "Ready. Run 'just check' to verify."

# Quality gates - add language-specific checks
check:
    @echo "Add fmt, lint, test recipes"

# Remove build artifacts
clean:
    @echo "Add clean commands"

See just-pro skill for language-specific recipes.

---

Step 5: Mise Configuration

Create .mise.toml:

[tools]
# Add tools with: mise use <tool>@<version>
# Examples:
# node = "22"
# go = "1.23"
# rust = "1.83"
# just = "latest"

---

Step 5.5: Output Compression (Optional)

CLI output compression reduces build/test/git noise before it reaches LLM context. See output-compression skill for full details.

# Option 1: RTK (zero-config baseline — recommended)
command -v rtk &>/dev/null && rtk init --global || echo "Install: brew install rtk"

# Option 2: tokf (per-project customization — add when RTK isn't enough)
command -v tokf &>/dev/null && tokf hook install || echo "Install: brew install mpecan/tokf/tokf"

Either or both tools can be active. RTK handles most CLI noise automatically. Add tokf with project-local .tokf/filters/ when you need surgical filtering for specific commands.

---

Step 6: Environment Template

Create .envrc.example (committed) as template for .envrc (gitignored):

# Copy to .envrc and fill in values
# cp .envrc.example .envrc && direnv allow

# Mise integration
if command -v mise &> /dev/null; then
  eval "$(mise hook-env -s bash)"
fi

# Project-specific environment
# export DATABASE_URL="postgres://localhost/myapp"
# export API_KEY=""

---

Step 7: Claude Code Project Settings

Create .claude/settings.local.json to wire DM orchestration, hooks, and session management for this project:

mkdir -p .claude

Write to .claude/settings.local.json:

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "",
        "hooks": [
          {
            "type": "command",
            "command": "if command -v timbers &>/dev/null && [ -d .timbers ]; then timbers prime; fi",
            "timeout": 10
          }
        ]
      }
    ],
    "Stop": [
      {
        "matcher": "",
        "hooks": [
          {
            "type": "command",
            "command": "if command -v timbers &>/dev/null && [ -d .timbers ]; then timbers hook run claude-stop; fi",
            "timeout": 30
          }
        ]
      }
    ]
  }
}

This wires session-start context recovery and session-end enforcement. DM plugin skills (browser-qa, evaluator, repo-init, language skills, architecture skills) are available globally from the plugin install — this file adds project-specific hooks.

Customize per-project: Add project-specific SessionStart commands (e.g., bd prime if beads is initialized), adjust Stop hook timeout for heavy gate suites.

---

Step 8: Beads Initialization

Beads supports two sync modes. Pick one before running bd init for a new project. Per upstream's docs/SYNC_CONCEPTS.md, canonical (refs/dolt/data) is the recommended mode for new repos; legacy (JSONL-in-git) is supported for compatibility with existing repos that use it.

Sync mode at a glance

	Canonical (recommended for new repos)	Legacy (JSONL-in-git, for existing repos)
Source of truth	Dolt state in refs/dolt/data git ref namespace on origin	.beads/issues.jsonl (committed)
.beads/issues.jsonl role	Passive local export (viewer, interchange, backup) — gitignored	Cross-clone transport — committed
Sync commands	bd dolt push (after bead work) / bd dolt pull (after git pull)	Pre-commit auto-export + post-merge auto-import hooks
Config	sync.remote set in .beads/config.yaml; export.auto = false	export.auto = true, export.git-add = true
Fresh-clone onboarding	bd bootstrap (auto-detects refs/dolt/data on origin)	bd bootstrap (auto-detects committed JSONL)
PR noise	None — bead state never appears in branch diffs	Every bead mutation produces JSONL diff

bd bootstrap is the universal entry point for both modes — it auto-detects which the repo is in. Prefer it over bd init / bd import for cloning.

Canonical mode (recommended)

# 1. Initialize beads — auto-detects git origin and sets sync.remote
bd init

# 2. Seed refs/dolt/data on the git remote (publishes Dolt history)
bd dolt push

# 3. Disable JSONL auto-export — JSONL is no longer your sync channel
bd config set export.auto false
bd config set export.git-add false

# 4. Gitignore the JSONL exports (local view, not transport)
cat >> .beads/.gitignore <<'EOF'
issues.jsonl
sync_base.jsonl
EOF

# 5. Set your role and confirm
bd config set beads.role maintainer  # or "contributor" for outside contributors
bd dolt remote list                   # should show origin

Daily flow:

• After making bead changes: bd dolt push
• After git pull (peer may have pushed bead work): bd dolt pull
• New clones: bd bootstrap — clones Dolt history from refs/dolt/data automatically

bd dolt push is load-bearing under canonical mode — it's the sync. It is not optional and not a no-op. Treat any ~/.claude/CLAUDE.md or per-repo directive that forbids bd dolt push as a hard conflict requiring user attention.

Verifying sync cleanliness. bd dolt push doubles as the divergence verifier: it's a no-op (Push complete. with no chunks transferred) when local Dolt already matches refs/dolt/data on origin, ships unpushed state otherwise, and surfaces auth / divergence / offline errors via stderr. Do not reach for bd dolt status for this check — in beads 1.0.4 it reports only engine info + data dir, nothing about remote-divergence state. Run bd dolt push at session-close, pre-merge, or anywhere you need "is canonical sync clean?" — no chunks transferred = clean.

If you wire bd dolt push / bd dolt pull into git hooks (pre-push / post-merge): surface failures, don't swallow them. The naive bd dolt push 2>/dev/null || true pattern silently regresses what JSONL transport made visible (sync failures used to show up as merge conflicts on .beads/issues.jsonl; under canonical they vanish into the void if hidden). Use a tempfile + warning pattern that doesn't block the git op:

# pre-push (mirror for post-merge with bd dolt pull):
if command -v bd >/dev/null 2>&1; then
  _bd_err=$(mktemp -t bd-dolt-push.err.XXXXXX 2>/dev/null || echo /tmp/bd-dolt-push.err)
  if ! bd dolt push 2>"$_bd_err"; then
    echo >&2 "beads: 'bd dolt push' failed (continuing with git push); see $_bd_err"
    echo >&2 "       or run 'bd dolt push' manually after resolving (often: 'bd dolt pull' first)."
  else
    rm -f "$_bd_err"
  fi
fi

The dev gets feedback, the git op still completes, and the failure log survives for diagnosis.

Legacy mode (JSONL-in-git, for existing repos)

bd init  # embedded Dolt is the default and works on macOS in 1.0+

bd init does several things automatically in beads 1.0+:

• Creates .beads/embeddeddolt/ (data, gitignored) and .beads/hooks/ (committed shims)
• Sets core.hooksPath = .beads/hooks (relative)
• Installs bd setup claude integration (CLAUDE.md beads section + .claude/settings.json)
• Enables export.auto = true and export.git-add = true — every bd mutation auto-exports .beads/issues.jsonl and stages it (60s throttle; pre-commit hook forces a flush)

Hooks and timbers (both modes)

After bd init, install timbers hooks if used (they detect core.hooksPath and append into .beads/hooks/pre-commit alongside the beads hook):

timbers hooks install

Quality gates and any other custom hook content go OUTSIDE the --- BEGIN/END BEADS INTEGRATION --- and --- BEGIN/END TIMBERS --- markers — bd hooks install --force and timbers hooks install both preserve user content outside their managed sections.

Hook structure (.beads/hooks/pre-commit):

# --- BEGIN BEADS INTEGRATION v1.0.x ---  (managed by bd hooks install)
# --- END BEADS INTEGRATION v1.0.x ---

# Quality gates (lint-staged, just check, etc.) — preserved across reinstalls

# --- timbers section (managed by timbers hooks install)
# --- end timbers section ---

Add a just hooks recipe for onboarding that re-runs bd hooks install --force --beads (idempotent — preserves user content). Verify with bd hooks list (shows shim version per hook) and git config core.hooksPath (should be .beads/hooks).

Note on core.hooksPath: bd hooks install --force may set this to an absolute path on first install. Fix to relative manually if needed: git config core.hooksPath .beads/hooks — relative is required for worktrees, which share repo config.

Migration: legacy → canonical

If an existing legacy-mode repo wants to move to canonical:

1. bd dolt push — seeds refs/dolt/data on origin from current local Dolt state
2. git rm --cached .beads/issues.jsonl and add the file to .beads/.gitignore
3. bd config set export.auto false && bd config set export.git-add false
4. Commit the gitignore + JSONL removal
5. Peer clones run bd dolt pull once to refresh local Dolt; they're now on canonical

Do this as a deliberate one-time migration, not a side-effect of other work.

---

Step 8.5: Timbers Initialization (Optional)

If the user wants structured development reasoning logs (what/why/how per commit):

# Check if installed
command -v timbers || echo "Install: brew install gorewood/tap/timbers"

# Initialize (creates .timbers/, .gitattributes, git hooks, Claude Code integration)
timbers init --yes --git-hooks

# Add onboarding snippet to AGENTS.md
timbers onboard --target agents >> AGENTS.md

This sets up:

• .timbers/ directory for entry storage
• Pre-commit hook (blocks commits when prior commits are undocumented)
• Post-commit hook (reminds to document)
• Claude Code Stop hook (blocks session end if pending entries)

Timbers captures the reasoning behind commits — the "why" that git log can't tell you. Entries are files in .timbers/ that sync via regular git push.

Optional: Create .timbersignore at repo root to extend the default skip rules (lockfiles, reverts are already skipped by default in v0.19+). Use gitignore-style patterns for files that should never require a timbers entry:

# Generated files that don't need reasoning documented
*.generated.ts
db/migrations/*.sql

Skip timbers entirely if the project is trivial or short-lived.

---

Step 8.7: Multi-Account GitHub Auth (Optional)

If the user works across multiple GitHub identities (personal + work, multiple orgs), per-repo SSH-key routing is necessary for canonical-mode beads sync to work — bd dolt push uses the standard git@github.com: URL and needs the right key.

The legacy pattern was Host github.<alias> blocks in ~/.ssh/config with rewritten remote URLs, but that locks the SSH alias into team-shared config and breaks for anyone else.

Modern git-native pattern: includeIf in ~/.gitconfig.

# ~/.gitconfig
[includeIf "gitdir:~/Projects/<org>/"]
    path = ~/.gitconfig-<org>

# ~/.gitconfig-<org>
[user]
    email = you@<org>-domain
[core]
    sshCommand = "ssh -i ~/.ssh/<org>_key -o IdentitiesOnly=yes -F /dev/null"

Any git operation under ~/Projects/<org>/ uses the per-account key. All URLs stay standard git@github.com:org/repo.git (no Host github.<alias> rewrites), so bd dolt push, gh, and other tooling work transparently.

The -o IdentitiesOnly=yes -F /dev/null flags matter — without them, ssh may try other keys first and trip GitHub's bad-key rate limiter.

Skip if the user only has one GitHub identity.

---

Step 9: Next Steps

Point user to language-specific setup:

Language	Next Step
Go	Invoke go-pro skill, run go mod init
Rust	Invoke rust-pro skill, run cargo init
TypeScript	Invoke typescript-pro skill, run npm init
Python	Invoke python-pro skill, run uv init

---

Quick Reference

# Full manual init sequence — pick canonical or legacy at the bd step (see Step 8)
git init
# Create .gitignore, .claudeignore, AGENTS.md, CLAUDE.md symlink, justfile, .mise.toml, .envrc.example

# Canonical sync mode (recommended for new repos):
bd init
bd dolt push                             # seed refs/dolt/data on origin
bd config set export.auto false
bd config set export.git-add false
echo -e "issues.jsonl\nsync_base.jsonl" >> .beads/.gitignore

# OR legacy sync mode (JSONL-in-git, for compatibility):
# bd init  # embedded Dolt default with export.auto=true

timbers init --yes --git-hooks           # appends into .beads/hooks/ alongside beads
timbers onboard --target agents >> AGENTS.md
mise use just@latest
# Then follow language skill for specifics

Monorepo Variant

For monorepos, the root gets:

• Root justfile with module imports (see just-pro monorepo patterns)
• Root .mise.toml with shared tooling
• Root .claudeignore combining patterns for all languages in the monorepo
• Single .beads/ at root

Each package gets:

• Package-local justfile
• Language-specific configs (Cargo.toml, package.json, etc.)