atomic-wiki

atomic-wiki is a skill for Claude Code, Codex from damusix/atomic-claude. It costs 204 tokens per session (1,895 once invoked), scanned A, original, MIT.

A conversational system for organizing notes, research, tickets, raw material, and other knowledge into wiki folders called buckets. A wiki is a collection of linked pages used to store and retrieve project knowledge.

In plain words
What is it for?
Use it to create or add capture areas, store notes and research, set up a project wiki, ask what the wiki knows, or check whether its contents are out of date.
Why use it?
It gives unstructured information a known place and routes it according to the project's wiki setup. It can also handle requests to refresh, summarize, or query the stored knowledge.

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/damusix/atomic-claude/atomic-wiki
Any agent
npx skills add damusix/atomic-claude --skill atomic-wiki
Clone the repo
git clone --depth 1 https://github.com/damusix/atomic-claude

Made for: Claude Code, Codex.

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 atomic-wiki

README.md
[![agentmods](https://agentmods.dev/badge/skills/damusix/atomic-claude/atomic-wiki.svg)](https://agentmods.dev/skills/damusix/atomic-claude/atomic-wiki)
Your own site
<a href="https://agentmods.dev/skills/damusix/atomic-claude/atomic-wiki"><img src="https://agentmods.dev/badge/skills/damusix/atomic-claude/atomic-wiki.svg" alt="Measured on agentmods" height="20"></a>
Per session 204 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,895 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. 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 5.1 $0.00204 $0.01895
Opus 5 $0.00102 $0.00948
Sonnet 5 $0.00041 $0.00379
Haiku 4.5 $0.00020 $0.00189

Measured 6d ago against content hash b83eca6fc17e, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-05, from the pricing page.

Security

Grade A, and why

atomic-wiki 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 6d 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.

context/skills/atomic-wiki/SKILL.md · 106 lines

How it starts

The opening of the file, as written. The whole thing — 106 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Auto-fires on:

  • "I want a place for my notes / research / tickets / raw dumps"
  • "create a space for [notes|tickets|research]" — any capture-intent phrase
  • "add a bucket", "add this to my wiki", "wiki this"
  • "set up a karpathy wiki", "karpathy realm", "set up a wiki for my projects"
  • "what does my wiki know about X"
  • "is my wiki stale"

Conversational entry point for wiki and capture-bucket operations. Code writes structure; the model writes meaning. Degrades gracefully when atomic binary is absent.

Realm resolution

Read the <wikis> block in ~/.claude/CLAUDE.md (outside <atomic>, CLI-managed). Each entry is a path to a registered wiki's index.md. The realm root is the directory containing wiki/index.md.

  • cwd under a realm root → that realm is active. Bucket operations target it.
  • No registered realm + setup intentatomic wiki scan --root <path> bootstraps. Ask which folder is the realm root if ambiguous.
  • atomic binary absent → say so; point at /refresh-wiki and docs/reference/realm-wiki.md. Do not hand-build the structure.

Pipeline routing

When a full inference run is needed (refresh, summarize, synthesize), detect scope and load the matching reference:

  1. Read <wiki-type> from the active wiki index (docs/wiki/index.md for repo scope, wiki/index.md for realm scope).
  2. Repo scope (<wiki-type>repo</wiki-type>) — the full per-repo pipeline lives at ~/.claude/skills/atomic-wiki/references/repo.md (installed location). A full refresh is triggered via /refresh-wiki, which dispatches atomic-wiki-inferrer to execute it.
  3. Realm scope (<wiki-type>realm</wiki-type>) — the wiki-output and bucket-synthesis pipelines live at ~/.claude/skills/atomic-wiki/references/realm.md (installed location). A full refresh is triggered via /refresh-wiki [root], which orchestrates scan/stale/offer and dispatches atomic-wiki-inferrer for each inference step.

The pipeline text lives only in the reference files (installed at ~/.claude/skills/atomic-wiki/references/) — not here, and not duplicated in the agent's system prompt. When an agentic inference run is needed, the agent resolves $HOME via Bash and reads the appropriate reference file at its absolute path, then executes it.

Read the full file on GitHub · 106 lines

Files

What ships with it

2 files 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. 6d ago First seen · 106 lines · 204 tokens per session scan A b83eca6fc17e

Subscribe to this mod's changes

atomic-wiki is a skill published in the GitHub repository damusix/atomic-claude (84 stars, last pushed today), licensed MIT. It adds 204 tokens to every session and 1,895 once invoked, about $0.0010 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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