graphify - SKILL.md Agent Skill

name: graphify description: | Turn any folder of code, docs, papers, or images into a queryable knowledge graph — interactive HTML, GraphRAG-ready JSON, and a plain-language audit report. allowed-tools: - Read - Write - Bash - Glob - Grep

/graphify

Turn any folder of files into a navigable knowledge graph with community detection, an honest audit trail, and three outputs: graph.html, graph.json, and GRAPH_REPORT.md.

Source: safishamsi/graphify

Usage

/graphify                         # full pipeline on current directory
/graphify <path>                  # full pipeline on specific path
/graphify <path> --mode deep      # thorough extraction, richer INFERRED edges
/graphify <path> --update         # incremental — re-process only changed files
/graphify <path> --no-viz         # skip HTML visualization, just report + JSON
/graphify <path> --svg            # also export graph.svg (embeds in Notion, GitHub)
/graphify <path> --neo4j          # generate cypher.txt for Neo4j import
/graphify <path> --watch          # watch folder, auto-rebuild on code changes
/graphify <path> --wiki           # build agent-crawlable wiki (index.md + per-community articles)
/graphify add <url>               # fetch URL, save to ./raw, update graph
/graphify query "<question>"      # BFS traversal — broad context
/graphify query "<question>" --dfs  # DFS — trace a specific path
/graphify explain "<Node>"        # plain-language explanation of a node
/graphify path "A" "B"            # shortest path between two concepts

What graphify is for

graphify is built around Andrej Karpathy's /raw folder workflow: drop anything into a folder — papers, code, screenshots, notes — and get a structured knowledge graph that shows you what you didn't know was connected.

Three things it does that Claude alone cannot:

Persistent graph — relationships are stored in graphify-out/graph.json and survive across sessions
Honest audit trail — every edge tagged EXTRACTED, INFERRED, or AMBIGUOUS
Cross-document surprise — community detection finds connections across files you'd never think to query

Step 1 — Ensure graphify is installed

# Detect the correct Python interpreter
PYTHON=""
GRAPHIFY_BIN=$(which graphify 2>/dev/null)
if [ -z "$PYTHON" ] && command -v uv >/dev/null 2>&1; then
    _UV_PY=$(uv tool run graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
    if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
fi
if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
    _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
    case "$_SHEBANG" in
        *[!a-zA-Z0-9/_.-]*) ;;
        *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
    esac
fi
if [ -z "$PYTHON" ]; then PYTHON="python3"; fi
"$PYTHON" -c "import graphify" 2>/dev/null \
  || "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
  || "$PYTHON" -m pip install graphifyy -q --break-system-packages 2>&1 | tail -3
mkdir -p graphify-out
"$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w').write(sys.executable)"

If graphify is not installed and pip fails, tell the user to install it:

uv tool install graphifyy   # recommended
# or: pipx install graphifyy
# or: pip install graphifyy

In all subsequent steps, replace python3 with $(cat graphify-out/.graphify_python).

Step 2 — Detect files

$(cat graphify-out/.graphify_python) -c "
import json
from graphify.detect import detect
from pathlib import Path
result = detect(Path('INPUT_PATH'))
print(json.dumps(result))
" > graphify-out/.graphify_detect.json

Replace INPUT_PATH with the path the user provided (default: .). Read the JSON silently and present a clean summary:

Corpus: X files · ~Y words
  code:    N files (.py .ts .go ...)
  docs:    N files (.md .txt ...)
  images:  N files

Omit categories with 0 files. Then:

If total_files is 0: stop with "No supported files found in [path]."
If total_words > 2,000,000 or total_files > 200: list the top 5 subdirs by file count and ask the user which subfolder to run on. Wait for their answer.
Otherwise: proceed to Step 3.

Step 3 — Build the graph

$(cat graphify-out/.graphify_python) -m graphify INPUT_PATH [FLAGS]

Pass through any flags the user specified (--mode deep, --update, --no-viz, etc.). This runs the full pipeline: AST extraction, LLM concept/relationship extraction via Claude subagents, Leiden community detection, and export.

Stream output so the user can see progress. The pipeline can take several minutes on large corpora.

Step 4 — Report results

After the pipeline completes, read graphify-out/GRAPH_REPORT.md and present:

God nodes — the most-connected concepts (the structural backbone of the codebase)
Surprising connections — edges between concepts you'd expect to be unrelated
Community summary — what each cluster contains
Suggested questions — from the report's recommended queries

Then tell the user:

graphify-out/graph.html — open in any browser for interactive exploration
graphify-out/graph.json — persistent graph, queryable with /graphify query
graphify-out/GRAPH_REPORT.md — plain-language audit

Ask: "Want me to add a rule so Claude references this graph in future sessions?" If yes, create .claude/rules/graphify.md with:

Reference graphify-out/graph.json and graphify-out/GRAPH_REPORT.md for knowledge graph context.
Use /graphify query "<question>" to traverse the graph before exploring unfamiliar code paths.

Create .claude/rules/ if needed.

Tips

Use --update for incremental runs — only changed files are re-processed
Use --mode deep on smaller corpora for richer relationship extraction
graphify add <url> fetches a URL and adds it to the graph without a full rebuild
.graphifyignore excludes paths (same syntax as .gitignore)
The graph persists across sessions — graph.json is your queryable index