semantic-clusters

semantic-clusters is a skill for Claude Code, Codex from DojoGenesis/mcp. It costs 129 tokens per session (3,322 once invoked), scanned A, original, MIT.

A method for mapping a software system by the actions its parts perform instead of by their folders.

In plain words
What is it for?
Use it to create a behavioral architecture map, find capability gaps, and understand how components work together.
Why use it?
It reveals capabilities that cross multiple directories and exposes missing, duplicated, or confusing areas of the design.

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/dojogenesis/mcp/semantic-clusters
Any agent
npx skills add DojoGenesis/mcp --skill semantic-clusters
Clone the repo
git clone --depth 1 https://github.com/DojoGenesis/mcp

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 semantic-clusters

README.md
[![agentmods](https://agentmods.dev/badge/skills/dojogenesis/mcp/semantic-clusters.svg)](https://agentmods.dev/skills/dojogenesis/mcp/semantic-clusters)
Your own site
<a href="https://agentmods.dev/skills/dojogenesis/mcp/semantic-clusters"><img src="https://agentmods.dev/badge/skills/dojogenesis/mcp/semantic-clusters.svg" alt="Measured on agentmods" height="20"></a>
Per session 129 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,322 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 $0.00129 $0.03322
Opus 5 $0.00064 $0.01661
Sonnet 5 $0.00026 $0.00664
Haiku 4.5 $0.00013 $0.00332

Measured 3d ago against content hash cfbeb0585273, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

semantic-clusters 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 3d 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.

internal/skills/bundled/system-health/semantic-clusters/SKILL.md · 273 lines

How it starts

The opening of the file, as written. The whole thing — 273 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Semantic Clusters Skill

Version: 1.0 Created: 2026-02-11 Purpose: Map software systems by behavioral capabilities using action-verb clusters, revealing what a system does rather than where its files live.


I. The Philosophy: Behavior Over Location

Every codebase has two architectures:

  1. The filesystem architecture -- where files live. Directories, packages, modules. This is what ls shows you.
  2. The behavioral architecture -- what the system does. Capabilities that cross-cut directories, features that span layers.

Most people only see architecture #1. They think in terms of frontend/, backend/, utils/. But understanding comes from architecture #2 -- the verbs.

A "chat" feature isn't in one directory. It's a component in the frontend, a handler in the backend, a state engine in a context, a streaming service, an SSE connection, and a set of tools. These parts live in 6 different directories. But they all serve one verb: CONVERSE.

Semantic clusters make the behavioral architecture visible. Each cluster is named with an action verb, and every significant component in the codebase maps to one (sometimes two) clusters. The result is a map of what the system can do -- not just where its files happen to be.

This distinction matters because:

  • Refactoring within a cluster is safer than refactoring across clusters. Components in the same cluster share a purpose; changing them together makes sense.
  • Gaps become visible. If you have PERSIST but no PROTECT, you're storing data without security boundaries.
  • Coupling is explicit. Cross-cluster components are integration points where changes propagate. You can see them in the map instead of discovering them during a production incident.
  • Onboarding improves. "Let me explain what this system can DO" is a better orientation than "let me show you the directory tree."

II. When to Use This Skill

  • Exploring a new codebase: Before diving into files, map the behavioral capabilities to build your mental model.
  • Explaining a system: Clusters make better explanations than directory trees because they answer "what does it do?" not "where are the files?"
  • Planning a refactor: Clusters reveal which components serve the same capability. Refactoring within a cluster is safer than across clusters.
  • Auditing feature coverage: Clusters expose gaps -- capabilities the system lacks or has only partially implemented.
  • Identifying architectural confusion: If a component maps to 3+ clusters, it's probably doing too much. If a directory has components in 5 different clusters, it may need restructuring.
  • Writing status documents: The behavioral architecture section of a STATUS.md uses clusters.
  • Sprint planning: Assign work by cluster. "This sprint we're focused on OBSERVE and PRESENT."
  • Code review: Ask "which clusters does this PR touch?" A PR that modifies 4+ clusters deserves extra scrutiny.
  • Technical debt tracking: Rate each cluster's health independently. Focus debt reduction on unhealthy clusters.

Read the full file on GitHub · 273 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. 3d ago First seen · 273 lines · 129 tokens per session scan A cfbeb0585273

Subscribe to this mod's changes

semantic-clusters is a skill published in the GitHub repository DojoGenesis/mcp (0 stars, last pushed 1mo ago), licensed MIT. It adds 129 tokens to every session and 3,322 once invoked, about $0.0006 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 2026-08-31.

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