repo-init

repo-init is a skill for Claude Code from dgilford/ai-science-toolkit. It costs 67 tokens per session (2,829 once invoked), scanned A, original, MIT.

A slash command that adds a standard project structure to a new or existing repository. It can set up either a research project or a distributable package, and previews changes with a dry run.

In plain words
What is it for?
Use it to initialize research repositories, create Python-style package layouts, inspect the planned setup, or add missing standard files to an existing repository.
Why use it?
It provides a repeatable starting structure while avoiding overwriting files that already exist.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter. Also seen: mentions CLAUDE.md; mentions AGENTS.md.

Runs only inside its plugin — its command needs a path that Claude Code sets for a plugin’s own hooks and for nothing else. Install the plugin, not this.

Part of the ai-science-toolkit plugin — 21 skills, 4 agents shipped together

Good fit Use it to initialize research repositories, create Python-style package layouts, inspect the planned setup, or add missing standard files to an existing repository.

Compare 6 skills from other repositories ↓
Install

Getting it into your agent

This one installs as part of its plugin. Adding the marketplace and installing the plugin brings it with everything else the plugin ships.

Claude Code
/plugin marketplace add dgilford/ai-science-toolkit
Claude Code
/plugin install ai-science-toolkit

Made for: Claude Code.

Or install ai-science-toolkit, the plugin that ships this one along with the rest of its 21 skills, 4 agents.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for repo-init

README.md
[![agentmods](https://agentmods.dev/badge/skills/dgilford/ai-science-toolkit/repo-init/github.svg)](https://agentmods.dev/skills/dgilford/ai-science-toolkit/repo-init)
Your own site
<a href="https://agentmods.dev/skills/dgilford/ai-science-toolkit/repo-init"><img src="https://agentmods.dev/badge/skills/dgilford/ai-science-toolkit/repo-init/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for repo-init

Your own site · 80×15
<a href="https://agentmods.dev/skills/dgilford/ai-science-toolkit/repo-init"><img src="https://agentmods.dev/badge/skills/dgilford/ai-science-toolkit/repo-init.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 67 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,829 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00067 $0.02829
Opus 5 $0.00034 $0.01414
Sonnet 5 $0.00013 $0.00566
Haiku 4.5 $0.00007 $0.00283

Measured 12d ago against content hash 5f4339f10b6f, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

repo-init scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/repo-init/SKILL.md · 102 lines

How it starts

The opening of the file, as written. The whole thing — 102 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Initialize a repository with a standard, opinionated project structure. Run once per project. Re-running (or running on an existing repo) adds missing pieces only — it never overwrites or repairs existing files.

The intake is a hard gate. Create nothing — no directories, no files, not even git init — until the step-2 intake is either completed with the user or skipped by an explicit flag (--no-grill / --dry-run). Scaffolding first and asking later defeats the skill: the answers determine what gets scaffolded.

File templates (loaded at runtime)

D="${CLAUDE_PLUGIN_ROOT:+$CLAUDE_PLUGIN_ROOT/skills/repo-init}"; D="${D:-$HOME/.claude/skills/repo-init}"; cat "$D/TEMPLATES.md" 2>/dev/null || echo "(TEMPLATES.md not found — abort and report a broken install)"

Live state

pwd && git rev-parse --show-toplevel 2>/dev/null || echo "(not a git repo yet)"

Modes

Invocation Mode Shape
/repo-init research (default) Analysis project: notebooks, script-first compute, gitignored data/figures
/repo-init --package package Distributable library: src-layout, pyproject, tests, CI, CITATION.cff
[path] either Target directory (default: cwd). Must exist or be creatable.
--no-license either Skip the LICENSE file and the pyproject/CITATION license fields.
--no-grill either Skip the intake grill; scaffold with template stubs as-is (LICENSE defaults to MIT with the git author as holder — flagged in the report).
--dry-run either Print the would-be report (every path → created/skipped) for the flag-resolved mode, without writing anything, running git init, or grilling. (Since the grill is skipped, decisions it would set — mode flip, license, data guards — are not previewed.)

Ground rules

  1. Never destructive. Before writing any file: if it already exists, skip it — never overwrite, never merge silently. mkdir -p for directories is always fine. Report skipped (exists); reserve skipped (exists — differs from template) for files that look like a broken or partial scaffold (unfilled placeholders, a template skeleton with no real content). Pre-existing real content is normal, not a warning.
  2. Two sanctioned exceptions to "never touch an existing file":
    • .gitignore — never rewrite; diff it against the template entries, report which standard entries are missing, and ask before appending (gitignoring is a deliberate choice). After any append, run git ls-files against the newly ignored patterns: if matches exist, warn explicitly that .gitignore does not untrack already-committed files (they stay in the repo and its history until git rm --cached / a history rewrite) — this matters most before a repo ever goes public.
    • docs/DECISIONS.md — an append-only ledger: a re-run appends a new dated init entry recording that run's intake answers; existing entries are never edited or rewritten.
  3. CLAUDE.md / AGENTS.md on retrofit: if CLAUDE.md already exists and is not the redirect stub (compare against the CLAUDE-STUB template), do not create AGENTS.md — ask the user: keep CLAUDE.md canonical (scaffold no AGENTS.md, or an inverted 3-line AGENTS.md stub pointing at CLAUDE.md), or migrate to the AGENTS-canonical pattern. Never leave both files substantive — that split-brain is exactly what the redirect convention exists to prevent.
  4. Substitute all {{PLACEHOLDERS}} and <angle-bracket> fills per the header of TEMPLATES.md before writing. {{AUTHOR}}/{{EMAIL}} come from git config user.name/user.email; if unset, use a <fill me in> placeholder and flag it in the report. If the intake changes the mode, redo step-1 resolution (including {{PKG_NAME}}) before scaffolding.

Read the full file on GitHub · 102 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 12d ago First seen · 102 lines · 67 tokens per session scan A 5f4339f10b6f

Subscribe to this mod's changes

repo-init is a skill published in the GitHub repository dgilford/ai-science-toolkit (62 stars, last pushed 23d ago), licensed MIT. It adds 67 tokens to every session and 2,829 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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