Wire Gemini CLI to a knowledge graph of your repo

Gemini CLI explores a codebase the way most terminal agents do: it lists directories, opens files, and holds what it read in context. Graphify gives it a second, cheaper option: a local knowledge graph in graphify-out/ that it can query for exact structure. The Gemini CLI integration uses two native mechanisms at once: always-on rules in GEMINI.md, and a BeforeTool hook that fires right before the agent reads a file or lists a directory.

What graphify gemini install writes

• The skill: ~/.gemini/skills/graphify/SKILL.md on macOS and Linux (~/.agents/skills/graphify/SKILL.md on Windows, where Gemini CLI searches that path with higher priority). This is what /graphify triggers.
• A GEMINI.md section: query-first rules in your project's GEMINI.md, so every conversation starts knowing the graph exists. The installer owns only its own section; the rest of the file is untouched.
• A BeforeTool hook in .gemini/settings.json: it matches read_file|list_directory and runs graphify hook-guard gemini just before those tools execute.

## graphify This project has a knowledge graph at graphify-out/ with god nodes,community structure, and cross-file relationships. Rules:- For codebase questions, first run `graphify query "<question>"`  when graphify-out/graph.json exists. Use `graphify path "<A>" "<B>"`  for relationships and `graphify explain "<concept>"` for focused  concepts.

Set it up

1. Install the CLI. If graphify is not found afterwards, run uv tool update-shell and open a new terminal.
2. From the project root: graphify gemini install. Prefer everything inside the repo? graphify gemini install --project writes the skill under .gemini/skills/ and prints a git add hint, so the setup is committable.
3. Build the graph: type /graphify . in a Gemini CLI session. It writes graphify-out/ with graph.json (the queryable graph), graph.html (interactive), and GRAPH_REPORT.md (highlights, suggested questions).
4. Ask something structural and watch the agent query the graph first.

$ uv tool install graphifyy$ graphify gemini install

/graphify .

How the BeforeTool hook works

Gemini CLI exposes hooks that run before tool calls, and Graphify uses exactly one of them. Right before the agent runs read_file or list_directory, the hook checks whether graphify-out/graph.json exists. If it does, the tool call proceeds with a reminder attached: run graphify query "<question>" for a scoped subgraph instead of walking raw files. If there is no graph yet, the hook stays silent, so an uninitialized repo behaves exactly as before.

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

The hook never blocks: it always allows the tool call and only adds context. It is a shell-agnostic graphify subcommand rather than inline shell, so it behaves the same on macOS, Linux, and Windows, and the installer re-registers it on every run so an upgraded CLI never leaves a stale hook payload behind. In the installed file the command embeds the absolute path to your graphify executable.

Query results come back with file:line citations, and every edge is tagged EXTRACTED, INFERRED, or AMBIGUOUS, so the agent knows what was parsed from the AST versus connected by a model. The full command set is in the CLI reference.

Gemini CLI vs Google Antigravity

These are two different Graphify platforms. graphify gemini installcovers the Gemini CLI terminal agent described on this page. Google Antigravity, Google's agentic IDE, has its own installer (graphify antigravity install) that writes .agents rules and workflows instead, and its global skill lives at ~/.gemini/config/skills/. If you use both, install both; see Graphify + Google Antigravity.

Keeping the graph current

After code changes, graphify update . re-extracts only the files that changed (AST-only, no API cost); the GEMINI.md rules tell the agent to run it after modifying code. graphify hook install adds post-commit and post-checkout git hooks that do the same automatically.

Troubleshooting

• graphify: command not found: the uv or pipx tool bin dir (~/.local/bin) is not on your PATH yet. Run uv tool update-shell (or pipx ensurepath) and open a new terminal.
• No nudge appears before reads: that is expected until graphify-out/graph.json exists. The hook is deliberately silent without a graph, so build one with /graphify . first.
• /graphify does nothing: confirm the skill file exists (~/.gemini/skills/graphify/SKILL.md, or ~/.agents/skills/ on Windows) and that GEMINI.md contains the graphify section, then start a new session.
• Hook stopped firing after an upgrade: the hook command embeds the absolute executable path at install time. Re-run graphify gemini install; it replaces its own hook entry idempotently.
• The graph lives somewhere else: the hook honors the GRAPHIFY_OUT environment variable when your output directory is not the default graphify-out/.

Gemini CLI FAQ

Next steps

The quickstart walks the whole flow from install to first query, and the CLI reference covers every command the rules point Gemini CLI at. The same graph serves your other assistants too: see Graphify + Claude Code, Graphify + Codex, or browse every assistant on the integrations page.