graphify

A tool that turns a folder or code repository into a knowledge graph, a map showing relationships between files and information.

In plain words
What is it for?
It is for creating an interactive HTML graph, data for GraphRAG systems that retrieve related information, and a plain-language report. It can process local folders, GitHub repositories, multiple repositories, or changed files.
Why use it?
It helps people navigate large collections of files and see how their parts connect, with a record of how each connection was found.

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/agent-hellboy/mcp-runtime/graphify
Any agent
npx skills add Agent-Hellboy/mcp-runtime --skill graphify
Clone the repo
git clone --depth 1 https://github.com/Agent-Hellboy/mcp-runtime

Made for: Claude Code, Codex.

Per session 55 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 13,854 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. Scan, not verified.
Origin 88% copy Near-identical to another mod 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 $0.00055 $0.13854
Opus 5 $0.00028 $0.06927
Sonnet 5 $0.00011 $0.02771
Haiku 4.5 $0.00006 $0.01385

Measured yesterday against content hash d7f2ca55f0c9, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

graphify scanned grade A 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.

Unrestricted tool accesslowExcessive agency

A wildcard tool grant or "run any command" leaves no least-privilege boundary at all.

If the user invoked `/graphify --help` or `/graphify -h` (with no other arguments), print the contents of the `## Usage` section above verbatim and stop. Do not run any commands, do not detect files, do not default the p

Downgraded: this mod is about security review, or the phrase is quoted, so it is likely naming the pattern rather than instructing it.

Origin

This is a copy

88% identical to graphify — 641 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

.codex/skills/graphify/SKILL.md · 1,115 lines

How it starts

The opening of the file, as written. The whole thing — 1,115 lines — stays where its author put it; the contents beside it link to each section on GitHub.

/graphify

Turn any folder of files into a navigable knowledge graph with community detection, an honest audit trail, and three outputs: interactive HTML, GraphRAG-ready JSON, and a plain-language GRAPH_REPORT.md.

Usage

/graphify                                             # full pipeline on current directory → Obsidian vault
/graphify <path>                                      # full pipeline on specific path
/graphify https://github.com/<owner>/<repo>           # clone repo then run full pipeline on it
/graphify https://github.com/<owner>/<repo> --branch <branch>  # clone a specific branch
/graphify <url1> <url2> ...                           # clone multiple repos, build each, merge into one cross-repo graph
/graphify <path> --mode deep                          # thorough extraction, richer INFERRED edges
/graphify <path> --update                             # incremental - re-extract only new/changed files
/graphify <path> --directed                            # build directed graph (preserves edge direction: source→target)
/graphify <path> --whisper-model medium                # use a larger Whisper model for better transcription accuracy
/graphify <path> --cluster-only                       # rerun clustering on existing graph
/graphify <path> --no-viz                             # skip visualization, just report + JSON
/graphify <path> --html                               # (HTML is generated by default - this flag is a no-op)
/graphify <path> --svg                                # also export graph.svg (embeds in Notion, GitHub)
/graphify <path> --graphml                            # export graph.graphml (Gephi, yEd)
/graphify <path> --neo4j                              # generate graphify-out/cypher.txt for Neo4j
/graphify <path> --neo4j-push bolt://localhost:7687   # push directly to Neo4j
/graphify <path> --mcp                                # start MCP stdio server for agent access
/graphify <path> --watch                              # watch folder, auto-rebuild on code changes (no LLM needed)
/graphify <path> --wiki                               # build agent-crawlable wiki (index.md + one article per community)
/graphify <path> --obsidian --obsidian-dir ~/vaults/my-project  # write vault to custom path (e.g. existing vault)
/graphify add <url>                                   # fetch URL, save to ./raw, update graph
/graphify add <url> --author "Name"                   # tag who wrote it
/graphify add <url> --contributor "Name"              # tag who added it to the corpus
/graphify query "<question>"                          # BFS traversal - broad context
/graphify query "<question>" --dfs                    # DFS - trace a specific path
/graphify query "<question>" --budget 1500            # cap answer at N tokens
/graphify path "AuthModule" "Database"                # shortest path between two concepts
/graphify explain "SwinTransformer"                   # plain-language explanation of a node

Read the full file on GitHub · 1,115 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. yesterday First seen · 1,115 lines · 55 tokens per session scan A d7f2ca55f0c9

Subscribe to this mod's changes

graphify is a skill published in the GitHub repository Agent-Hellboy/mcp-runtime (5 stars, last pushed 7d ago), licensed Apache-2.0. It adds 55 tokens to every session and 13,854 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (unrestricted tool access). It is 88% identical to graphify, differing in 641 lines, and is treated as a copy.

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