deep-init

deep-init is a command for Claude Code from reese-allison/claude-tools. It costs 32 tokens per session (1,396 once invoked), scanned A, original, MIT.

A command that generates CLAUDE.md instruction files throughout a repository. It examines the repository structure to find directories where local context would help the coding agent.

In plain words
What is it for?
Use it without an argument to process the repository, or provide a path to generate instructions for one directory.
Why use it?
It gives the agent guidance closer to the code it is editing, which can prevent errors caused by treating every directory as if it followed the same rules.

Command for Claude Code

Written for Claude Code: disable-model-invocation in frontmatter. Also seen: mentions CLAUDE.md; mentions subagents; mentions AGENTS.md.

Part of the deep-init plugin — 1 command shipped together

Good fit Use it without an argument to process the repository, or provide a path to generate instructions for one directory.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/reese-allison/claude-tools/init
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.

Clone the repo
git clone --depth 1 https://github.com/reese-allison/claude-tools

Made for: Claude Code.

Or install deep-init, the plugin that ships this one along with the rest of its 1 command.

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 deep-init

README.md
[![agentmods](https://agentmods.dev/badge/commands/reese-allison/claude-tools/init/github.svg)](https://agentmods.dev/commands/reese-allison/claude-tools/init)
Your own site
<a href="https://agentmods.dev/commands/reese-allison/claude-tools/init"><img src="https://agentmods.dev/badge/commands/reese-allison/claude-tools/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 deep-init

Your own site · 80×15
<a href="https://agentmods.dev/commands/reese-allison/claude-tools/init"><img src="https://agentmods.dev/badge/commands/reese-allison/claude-tools/init.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 32 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 1,396 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 $0.00032 $0.01396
Opus 5.5 $0.00013 $0.00558
Sonnet 5.5 $0.00006 $0.00279
Haiku 4.5 $0.00003 $0.00140

Measured 2mo ago against content hash dd5efd3a5266, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

deep-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 2mo 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.

deep-init/commands/init.md · 151 lines

How it starts

The opening of the file, as written. The whole thing — 151 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Deep Init - Hierarchical CLAUDE.md Generation

Arguments: $ARGUMENTS (optional path for single directory)

Flow:

  • No args → Run Phase 1-3
  • With path → Skip to Phase 3 for that path only

Phase 1: Discovery

Skip if $ARGUMENTS has path.

Step 1a: Structure

Build the directory tree from git-tracked files:

git ls-files | xargs -n1 dirname | sort | uniq -c | sort -rn

For each directory, capture:

  • path - Directory path
  • files - List of git-tracked filenames in this dir
  • file_count - Number of direct files
  • subtree_file_count - Total files in subtree
  • has_manifest - Contains package.json, go.mod, Cargo.toml, pyproject.toml, etc.
  • has_readme - Contains README.md

Step 1b: Semantic Context (if tools available)

If you have access to tools that can extract symbol signatures (class/function/type names) without reading full file contents, use them on directories with ≥3 files to gather:

  • symbols - List of symbol names and their kinds
  • domain_hints - Inferred from symbol names (e.g., AuthService → auth domain, StripeClient → integration)

This helps identify domain boundaries and integration points that aren't obvious from filenames alone.

Output: JSON tree structure with all directories and metadata (including symbols if available).


Phase 2: Judgment

Skip if $ARGUMENTS has path - use that as sole target.

Examine the full tree recursively. Identify directories warranting CLAUDE.md.

A directory qualifies if it is ANY of:

  1. DOMAIN BOUNDARY - Distinct conceptual area (auth, billing, search). Cohesive files that belong together. Someone would work "in this domain."

  2. INTEGRATION POINT - Connects to external systems. File names suggest external communication (webhook, client, adapter, api). Own config for external services.

  3. SUB-APP - Self-contained application. Has entry points, routes, or own runtime. Could be extracted as standalone.

  4. TECHNICAL COMPLEXITY - Specialized knowledge required. Non-obvious patterns that an AI agent would get wrong without guidance.

Read the full file on GitHub · 151 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. 2mo ago First seen · 151 lines · 32 tokens per session scan A dd5efd3a5266

Subscribe to this mod's changes

deep-init is a command published in the GitHub repository reese-allison/claude-tools (9 stars, last pushed 9mo ago), licensed MIT. It adds 32 tokens to every session and 1,396 once invoked, about $0.0001 per session on Opus 5.5. 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 2026-08-31.

Related

deep-init compared with commands from other repositories

deep-init next to 6 commands from other repositories
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deep-initreese-allison/claude-toolsCommand99mo agoMITA32Claude Code
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