Graphify CLI reference

The package is graphifyy and the command is graphify. Run commands from your project root; every reading command looks for graphify-out/graph.json unless you pass --graph PATH. This page is checked against graphify --help for version 0.9.97. Run graphify --version to see yours.

Skill or command? /graphify . is a message to your coding agent, which then runs these commands for you. graphify extract . is the shell command itself. Both write the same graphify-out/ folder.

Commands at a glance

Task	Command
Build a graph	`extract`, `update`, `watch`
Ask the graph	`query`, `explain`, `path`, `affected`, `god-nodes`
Communities	`cluster-only`, `label`
Work memory	`save-result`, `reflect`
Outputs	`export`, `tree`, `benchmark`
Many repositories	`global`, `merge-graphs`, `clone`
Automation	`hook`, `<agent> install`, `check-update`
Models	`provider`. See LLM providers

query, path, and explain exit 0 with an answer, 3 when a name matches several nodes (the candidates are printed), and 4 when nothing matches. Scripts can branch on these codes.

graphify extract

Headless build for CI and scripts: tree-sitter parsing for code, plus semantic extraction for docs, papers, and images.

graphify extract . --code-only

Flag	Default	What it does
`--code-only`	off	Index code only. No model or API key needed.
`--backend B`, `--model M`	auto-detect	Choose the model for semantic extraction.
`--mode deep`	off	More aggressive `INFERRED` edges from semantic extraction.
`--exclude PATTERN`	none	Skip matching paths. Repeatable, anchored at the root.
`--no-gitignore`	off	Ignore `.gitignore` and `.git/info/exclude`.
`--force`	off	Full re-scan, skipping incremental and semantic caches.
`--max-workers N`	CPU count	AST processes.
`--token-budget N`	`60000`	Token cap per semantic chunk.
`--max-concurrency N`	`4`	Parallel semantic chunks. Use `1` for local models.
`--api-timeout S`	`600`	Seconds per model request.
`--out DIR`	the scan path	Write `<DIR>/graphify-out/`.
`--no-cluster`	off	Skip clustering and write the raw extraction.
`--google-workspace`	off	Export Google Docs, Sheets, and Slides shortcuts first.
`--postgres DSN`	none	Add tables, views, functions, and foreign keys from a live PostgreSQL database.
`--cargo`	off	Add crate-to-crate dependencies from `Cargo.toml`.
`--global`, `--as TAG`	off	Also merge the result into the global graph.

graphify update <path> re-extracts changed code without a model, and graphify watch <path> does it on every save. Both accept --force and --no-cluster. See Incremental updates.

graphify query

Traverses the graph from the nodes whose labels match words in your question.

graphify query "cluster leiden" --budget 1000

Flag	Default	What it does
`--budget N`	`2000`	Cap the answer at N tokens.
`--dfs`	breadth-first	Follow one branch deep instead of the nearest neighbors.
`--seed X`	keyword matches	Start at a node id, label, or file path. Repeatable.
`--context C`	all	Only follow edges with this context. Repeatable.
`--graph PATH`	`graphify-out/graph.json`	Graph to read.

Matching uses label words, not full sentences. If you get exit code 4, use names from your code.

graphify explain

A plain-language summary of one node and its neighbors.

graphify explain "build_graph"
graphify explain "build_graph" --all

By default, the 20 most connected neighbors are listed; --all lists every connection.

graphify path

The shortest path between two nodes.

graphify path "extract" "cluster"

The search follows edge direction by default. Pass --undirected to ignore direction; --directed forces the default.

graphify affected

Walks edges in reverse to find what depends on a node.

graphify affected "load_config" --depth 3 --relation calls

--depth defaults to 2. --relation is repeatable. graphify god-nodes --top 10 [--json] lists the most connected nodes.

Clustering and labels

Command	What it does
`graphify cluster-only <path>`	Re-cluster an existing graph and rewrite the report. Flags: `--no-viz`, `--no-label`, `--backend`, `--model`, `--max-concurrency` (default 4), `--batch-size` (default 100).
`graphify label <path>`	Rename communities with the model. `--missing-only` keeps existing names.

Work memory

graphify save-result --question "Where is auth checked?" \
  --answer "middleware.verify_session" --nodes verify_session \
  --outcome useful
graphify reflect

--outcome is useful, dead_end, or corrected (with --correction TEXT). reflect writes graphify-out/reflections/LESSONS.md; --half-life-days (default 30) and --min-corroboration (default 2) tune it. See Work memory.

Exports

Command	Output
`graphify export html`	`graph.html` (`--node-limit`, default 5000)
`graphify export callflow-html`	Mermaid architecture and call-flow page
`graphify export obsidian`	Obsidian vault notes and canvas
`graphify export wiki`	Markdown wiki articles
`graphify export svg`, `graphml`	`graph.svg`, GraphML
`graphify export neo4j`, `falkordb`	Cypher, or `--push URI` to a database
`graphify tree`	`GRAPH_TREE.html` collapsible tree
`graphify benchmark`	Token use of the graph versus reading every file

For database pushes, set NEO4J_PASSWORD or FALKORDB_PASSWORD instead of passing --password, so it stays out of your shell history. See Exports.

Many repositories

graphify global add graphify-out/graph.json --as api
graphify global list
graphify merge-graphs a.json b.json --out combined.json
graphify clone https://github.com/Graphify-Labs/graphify

global remove TAG drops a repository; global path prints the global graph’s location (~/.graphify/global-graph.json).

Hooks and agents

Command	What it does
`graphify hook install`	Add post-commit, post-checkout, post-merge, and post-rewrite hooks, plus a merge driver for `graph.json`. `status` and `uninstall` too.
`graphify install [--platform P]`	Copy the skill for your agent. `uninstall` removes it everywhere (`--purge` also deletes `graphify-out/`).
`graphify claude install`, `cursor install`, `codex install`, and so on	Write the agent’s rules file and, where supported, a hook that points it at the graph.
`graphify check-update <path>`	Cron-safe check for pending semantic re-extraction.
`graphify prs`	Pull request dashboard. See PR impact.
`graphify add <url>`	Save a web page to `./raw` and update the graph.

Verify and troubleshoot

Symptom	Fix
`error: graph file not found`	Run `graphify extract .` first, or pass `--graph`.
Exit code `3`	Several nodes matched. Use a printed candidate or a file path.
A flag here is missing	Your version is older. Run `pip install -U graphifyy`.

What’s next

Environment variables

Settings for output, models, and hooks.

Ignoring files and limits

Control what gets scanned.

Try it in Graphify

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Features

Configuration

Support

Graphify CLI reference

Commands at a glance

graphify extract

graphify query

graphify explain

graphify path

graphify affected

Clustering and labels

Work memory

Exports

Many repositories

Hooks and agents

Verify and troubleshoot

What’s next

Environment variables

Ignoring files and limits

Try it in Graphify

​Commands at a glance

​graphify extract

​graphify query

​graphify explain

​graphify path

​graphify affected

​Clustering and labels

​Work memory

​Exports

​Many repositories

​Hooks and agents

​Verify and troubleshoot

​What’s next

Environment variables

Ignoring files and limits

Try it in Graphify

Commands at a glance

graphify extract

graphify query

graphify explain

graphify path

graphify affected

Clustering and labels

Work memory

Exports

Many repositories

Hooks and agents

Verify and troubleshoot

What’s next