> Graphify: the code knowledge graph for agents. Canonical: https://graphify.com/blog/gemini-cli-how-to-connect-graphify · Full index: https://graphify.com/llms-full.txt

# Gemini CLI: how to connect Graphify

*October 9, 2026 · Syed Fahad*

Gemini CLI can query a graph of the repository on your machine. Install Graphify, run `graphify gemini install`, and type `/graphify .` in a Gemini CLI session. The graph is written to `graphify-out/`. This path needs no Graphify account. The setup page is [Graphify + Gemini CLI](https://graphify.com/integrations/gemini-cli).

## Why Gemini CLI wants the graph

Gemini CLI lists directories and opens files, then holds what it read. A [code knowledge graph](https://graphify.com/blog/what-is-a-code-knowledge-graph) is the map of which function calls which, with a file and a line on each hop. Graphify builds that map on the machine, and the installer tells Gemini CLI to query it before it walks the tree.

## What you need

- Python 3.10 or later, and uv or pipx.
- Gemini CLI, already able to answer a normal prompt. Model access is Google's, separate from Graphify.
- The repository you want mapped.

## Install Graphify for Gemini CLI

```bash
uv tool install graphifyy
graphify gemini install
```

`pipx install graphifyy` is the other package install. The docs write the registration as `graphify install --platform gemini`. Both commands run the same installer.

From the project root, `graphify gemini install --project` keeps the skill in the repo at `.gemini/skills/graphify/SKILL.md`, so you can commit it.

If `graphify` is missing from the shell, run `uv tool update-shell` or `pipx ensurepath`, then open a new terminal.

## What the installer writes

The installer adds a skill, a section of `GEMINI.md`, and one hook. On an existing `GEMINI.md` it replaces only the section headed `## graphify`.

The skill goes to `~/.gemini/skills/graphify/SKILL.md` on macOS and Linux. On Windows it goes to `~/.agents/skills/graphify/SKILL.md`.

The `GEMINI.md` section tells the model to run `graphify query`, `graphify path`, and `graphify explain` when `graphify-out/graph.json` exists.

A BeforeTool hook lands in `.gemini/settings.json`. Before `read_file` or `list_directory`, Gemini CLI runs `graphify hook-guard gemini`. When the graph file exists, the hook attaches a reminder to query it, and the read still proceeds. When the graph file is absent, the hook stays quiet.

```json
{
  "hooks": {
    "BeforeTool": [
      {
        "matcher": "read_file|list_directory",
        "hooks": [
          { "type": "command", "command": "graphify hook-guard gemini" }
        ]
      }
    ]
  }
}
```

The installed command uses the absolute path to your `graphify` executable. Run the install again after an upgrade and it replaces that entry.

## Build the graph

In Gemini CLI, select the Graphify skill and enter:

```text
/graphify .
```

That writes `graphify-out/graph.json`, the file later queries read, plus `graphify-out/graph.html` and `graphify-out/GRAPH_REPORT.md`. The report lists highlights and questions worth asking next.

Code is parsed on the machine with tree-sitter. Docs and PDFs are read by the model you already use in Gemini CLI.

## Ask about the structure

Ask for a path through the code:

```text
Which modules read the payment config, and through what path?
```

From a terminal, once the graph exists:

```bash
graphify query "authentication flow"
```

Answers cite `file:line`. Each edge is tagged EXTRACTED when the parser found it, INFERRED when a model connected it, or AMBIGUOUS when the evidence did not resolve. Open the cited file before you rely on the answer.

After the code changes, `graphify update .` re-extracts the files that changed. `graphify hook install` adds post-commit and post-checkout git hooks that run the same update.

## Graphify Cloud uses a different install

The package [Graphify for Gemini CLI](https://github.com/Graphify-Labs/Graphify-gemini-extension) points Gemini CLI at the hosted server `https://api.graphify.com/mcp`.

```bash
gemini extensions install https://github.com/Graphify-Labs/Graphify-gemini-extension
```

Start a new Gemini CLI session and run `/mcp auth graphify`. Sign-in happens in the browser. The repository has to be indexed in Graphify Cloud first. That server is [Graphify MCP](https://graphify.com/mcp).

Google Antigravity has its own command, `graphify antigravity install`, and its own page, [Graphify + Google Antigravity](https://graphify.com/integrations/google-antigravity).

## If Gemini CLI misses the graph

- `graphify: command not found`: run `uv tool update-shell` or `pipx ensurepath`, then open a new terminal.
- `/graphify` does nothing: confirm the skill file and the graphify section in `GEMINI.md`, then start a new session.
- No reminder appears before a file read: build the graph first. The hook stays quiet until `graphify-out/graph.json` exists.
- The hook stops after an upgrade: run `graphify gemini install` again so the hook picks up the current executable path.
- The graph lives in another folder: set `GRAPHIFY_OUT` to that directory. The hook reads it.

`graphify gemini uninstall` removes the Gemini CLI registration. `graphify uninstall` removes Graphify from every assistant at once. Add `--purge` when you also want `graphify-out/` deleted.