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Gemini CLI: how to connect Graphify

· 4 minute read

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.

Why Gemini CLI wants the graphLink to Why Gemini CLI wants the graph

Gemini CLI lists directories and opens files, then holds what it read. 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 needLink to 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 CLILink to 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 writesLink to 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 graphLink to 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 structureLink to 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 installLink to Graphify Cloud uses a different install

The package Graphify for Gemini CLI 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.

Google Antigravity has its own command, graphify antigravity install, and its own page, Graphify + Google Antigravity.

If Gemini CLI misses the graphLink to 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.

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