deepinit

A repository documentation tool that creates linked AGENTS.md files for directories throughout a codebase. These files explain what each directory contains and how its code relates to the rest of the repository.

In plain words
What is it for?
Use it to document an entire nested repository, create or refresh an AGENTS.md tree, and help agents navigate related packages and directories.
Why use it?
A single documentation file can be insufficient for a large or multi-package repository. Directory-level guidance helps coding agents find the right instructions and preserves existing manual notes when documentation is regenerated.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/bobbyjohnstx/tinycode/deepinit
Any agent
npx skills add bobbyjohnstx/tinycode --skill deepinit
Clone the repo
git clone --depth 1 https://github.com/bobbyjohnstx/tinycode

Made for: Claude Code, Codex.

Per session 52 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,646 The whole file, excluding the scripts and references it only reads on demand.
Security scan C 1 finding. Scan, not verified.
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 $0.00052 $0.01646
Opus 5 $0.00026 $0.00823
Sonnet 5 $0.00010 $0.00329
Haiku 4.5 $0.00005 $0.00165

Measured yesterday against content hash 18417774fa26, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade C, and why

deepinit scanned grade C with 1 finding 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 yesterday.

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.

Hidden instructionshighPrompt injection

Directives inside HTML comments, invisible characters or bidirectional overrides are read by the model and not by the person reviewing the file.

grep -r "<!-- Parent:" --include="AGENTS.md" . ``` ## Smart Delegation | Task | Agent | |------|-------| | Directory mapping | `explore` | | File analysis | `architect` | | Content generation | `writer` | | AGENTS.md wri
packages/tinycode/src/skill/defaults/deepinit/SKILL.md · 219 lines

How it starts

The opening of the file, as written. The whole thing — 219 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Deep Init Skill

Creates comprehensive, hierarchical AGENTS.md documentation across the entire codebase.

Core Concept

AGENTS.md files serve as AI-readable documentation that helps agents understand:

  • What each directory contains
  • How components relate to each other
  • Special instructions for working in that area
  • Dependencies and relationships

When to Use

Use this skill when:

  • The user says "deepinit", "deep init", "document the whole repo", "AGENTS.md tree", or "per-directory docs"
  • The repo is large, nested, or multi-package and a single root CLAUDE.md is insufficient
  • You need agents to navigate documentation hierarchically (parent-to-child directory links)
  • You are initializing or refreshing AI-readable docs across an entire codebase
  • Existing AGENTS.md files need updating while preserving manual annotations

When Not to Use

  • A single root documentation file is all that's needed — use the init skill instead
  • The repo is trivial or flat (1–2 directories) — use init
  • The user wants to document a single file or answer a one-off question about the codebase
  • The request is to update one existing AGENTS.md by hand

Examples

Good: "Run deepinit on this monorepo — it has 8 packages and agents keep getting lost" → deepinit generates a parent-linked AGENTS.md tree across all packages.

Bad: "Initialize docs for this project" (small single-package repo with one src/ dir) → Use init to write a single CLAUDE.md instead.

Hierarchical Tagging System

Every AGENTS.md (except root) includes a parent reference tag:

<!-- Parent: ../AGENTS.md -->

This creates a navigable hierarchy:

/AGENTS.md                          ← Root (no parent tag)
├── src/AGENTS.md                   ← <!-- Parent: ../AGENTS.md -->
│   ├── src/components/AGENTS.md    ← <!-- Parent: ../AGENTS.md -->
│   └── src/utils/AGENTS.md         ← <!-- Parent: ../AGENTS.md -->
└── docs/AGENTS.md                  ← <!-- Parent: ../AGENTS.md -->

Read the full file on GitHub · 219 lines

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. yesterday First seen · 219 lines · 52 tokens per session scan C 18417774fa26

Subscribe to this mod's changes

deepinit is a skill published in the GitHub repository bobbyjohnstx/tinycode (11 stars, last pushed 4d ago), licensed MIT. It adds 52 tokens to every session and 1,646 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it C with 1 finding (hidden instructions). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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