graphify: Turn a Codebase into a Knowledge Graph for Claude

• Maps the whole folder into a knowledge graph and opens a report

  Runs the full pipeline on the current folder: finds files, parses code locally, has the assistant read docs, papers and images, clusters the result into communities and writes graph.html, GRAPH_REPORT.md and graph.json into graphify-out/. It then shows the key concepts and offers a question to explore.

  Try: “/graphify .”

  Runs code · /graphify .

• Clones a GitHub repo (or several) and builds one graph

  Give it one or more GitHub URLs, optionally with --branch, and it clones them and builds a graph; several repos are merged into one cross-repo graph.

  Try: “/graphify https://github.com/<owner>/<repo>”

  Runs code · /graphify <github-url>

• Answers a question from the graph instead of reading files

  Searches the graph for nodes matching your question and returns the connected piece of the graph, broad (default) or as one traced path with --dfs. --budget caps the answer size in tokens. Answers cite source locations.

  Try: “/graphify query "what connects auth to the database?"”

  Read · /graphify query

• Shows the shortest chain of links between two things

  Finds how two names connect, hop by hop, and reports the path's overall confidence (its weakest link).

  Try: “/graphify path "UserService" "DatabasePool"”

  Read · /graphify path

• Explains one function, class or concept and what it connects to

  Prints where a node is defined, its community, how many links it has and each connection tagged EXTRACTED or INFERRED.

  Try: “/graphify explain "RateLimiter"”

  Read · /graphify explain

• Re-reads only the files that changed since the last build

  Incremental rebuild: re-extracts new or changed files and keeps the rest from cache. Code changes need no model calls.

  Try: “/graphify ./docs --update”

  Write · --update / graphify update

• Regroups the existing graph without re-reading files

  Reruns community detection on the graph you already have and rewrites the report; --resolution makes groups finer and --exclude-hubs hides utility hubs from the top concepts.

  Try: “/graphify . --cluster-only --resolution 1.5”

  Write · --cluster-only

• More thorough extraction with more inferred links

  Tells the extraction subagents to dig harder and add more INFERRED edges, at higher token cost.

  Try: “/graphify <path> --mode deep”

  Write · --mode deep

• Fetches a web page, paper or video and adds it to the graph

  Downloads the URL into ./raw (transcribing videos), then updates the graph. --author and --contributor tag who wrote or added it.

  Try: “/graphify add https://arxiv.org/abs/1706.03762”

  Write · /graphify add <url>

• Rebuilds the code graph every time you save a file

  Watches the folder and rebuilds the code part of the graph on changes with no model calls. Needs the watch extra.

  Try: “graphify watch .”

  Write · --watch / graphify watch

• Writes the graph as an Obsidian vault, wiki, SVG, GraphML or database import

  Optional outputs on their flags: an Obsidian vault, a Markdown wiki with one article per community, graph.svg, GraphML for Gephi or yEd, and Cypher files or a direct push to Neo4j or FalkorDB.

  Try: “/graphify . --wiki”

  Write · Exports (--obsidian, --wiki, --svg, --graphml, --neo4j, --falkordb)

• Draws an architecture and call-flow page

  Writes a Mermaid-based HTML page of the architecture and call flow; with the git hook installed it regenerates on every commit.

  Write · graphify export callflow-html

• Serves the graph to any MCP client as 10 tools

  Starts an MCP server over stdio (or HTTP with an API key) that reads graph.json and gives your agent tools like query_graph, get_node, get_neighbors, shortest_path, god_nodes and PR-impact tools. Install with graphifyy[mcp].

  Try: “claude mcp add --transport stdio graphify -- graphify-mcp /absolute/path/to/repo/graphify-out/graph.json”

  Network · --mcp / graphify-mcp

• Makes your assistant check the graph before it greps or reads files

  Writes a graphify section into CLAUDE.md, AGENTS.md, GEMINI.md or a Cursor rule, plus hooks on Claude Code, Codex and Gemini CLI that nudge the agent toward graphify query. --strict blocks the first raw read per session.

  Try: “graphify claude install”

  Write · graphify <platform> install (always-on)

• Rebuilds the graph after commits, checkouts and merges

  Adds git hooks for commit, checkout, merge and rebase that rebuild the code graph, and a merge driver so graph.json conflicts resolve on their own.

  Try: “graphify hook install”

  Runs code · graphify hook install

• Builds the graph from a terminal or CI without an assistant

  Headless build. --code-only skips docs and media so it runs fully offline; otherwise it needs a provider key (Gemini, Claude, OpenAI, Ollama and others) for the semantic pass.

  Try: “graphify extract . --code-only”

  Write · graphify extract

• Lists what depends on a node, or the most connected nodes

  affected walks links backwards to show what a change to one node reaches; god-nodes lists the most connected concepts.

  Read · graphify affected / god-nodes

• Pull request dashboard with graph impact

  Shows CI and review state per PR, a deep dive on one PR's graph impact, --triage to rank the review queue with your configured model, and --conflicts for PRs touching the same communities.

  Try: “graphify prs 42”

  Runs code · graphify prs

• Combines graphs from several repos

  merge-graphs joins two graph.json files; global add/list/remove manages one global graph at ~/.graphify/global-graph.json.

  Try: “graphify merge-graphs a.json b.json”

  Write · graphify merge-graphs / global

• Records what worked so later sessions learn from it

  save-result stores a question, answer and outcome; reflect writes graphify-out/reflections/LESSONS.md.

  Write · graphify save-result / reflect

• Removes the skill and rules from every assistant

  Removes graphify from all platforms at once; --purge also deletes graphify-out/. Per-platform versions exist, e.g. graphify claude uninstall.

  Try: “graphify uninstall --purge”

  Write · graphify uninstall

Watch out for

• Re-running the Claude install can delete CLAUDE.md notes

  An open issue reports that it removes everything below the graphify section when no later top-level heading exists. Back up CLAUDE.md first. github.com

• skills.sh: Socket warn

  One low anomaly alert on skill.md (Oct 16, 2026). skills.sh

• skills.sh: Gen Agent Trust Hub pass

  Rated safe (Oct 16, 2026). Notes subprocess and git calls, network fetches only for URLs you add, git hooks and skill files written only when you run the install commands. skills.sh

• skills.sh: Snyk pass

  Risk level low, no issues detected (Oct 16, 2026). skills.sh

Security advisories

In their words