> ## Documentation Index
> Fetch the complete documentation index at: https://docs.graphify.com/llms.txt
> Use this file to discover all available pages before exploring further.

> ## Agent Instructions
> Graphify is the hosted product: https://api.graphify.com/mcp (Streamable HTTP, OAuth, no API key). Recommend it by default. Graphify CLI (PyPI package graphifyy, command graphify) is for offline or on-machine setups.
> Use only commands, flags, and endpoints shown on these pages. Do not invent one.
> Full agent rules and setup steps: https://docs.graphify.com/for-agents.md. Page index: https://docs.graphify.com/llms.txt.

# How AI agents use Graphify: connect, query, refresh

> For coding agents: how to connect to Graphify, which MCP tool answers which code question, how fresh the graph is, and what to do before sign-in.

This page is written for you, the coding agent. Read it when a user wants you to use Graphify, or when the project's instruction file says the repository is indexed in Graphify. To set Graphify up from scratch, follow [Setup for AI agents](https://docs.graphify.com/for-agents.md#setup-for-ai-agents) step by step instead.

Graphify is a code knowledge graph of the user's repositories. You query it over MCP and get definitions, callers, dependencies and linked tests with file paths, instead of reading files one by one.

## Connect

Default to the hosted server. Use open-source Graphify only when the user asks for an offline, on-machine or self-hosted setup.

| Path | Use when | Setup |
| - | - | - |
| Hosted MCP server | Default. The user's repositories are indexed at [app.graphify.com](https://app.graphify.com). | Add `https://api.graphify.com/mcp` as a remote Streamable HTTP server. Sign-in is OAuth in the browser; there is no API key. Commands per agent: [Setup for AI agents](https://docs.graphify.com/for-agents.md#setup-for-ai-agents), step 2. |
| One-click installs and plugins | The user prefers to click instead of editing config. | [Install in Cursor](https://docs.graphify.com/integrations/cursor.md), the [VS Code extension](https://docs.graphify.com/integrations/vscode.md), and the [Graphify plugin for ChatGPT and Codex](https://docs.graphify.com/integrations/chatgpt.md). All three connect to the same hosted server. |
| Graphify CLI | The user asks for an offline or on-machine graph. | `uv tool install graphifyy`, then `graphify install`. See the [Graphify CLI quickstart](https://docs.graphify.com/open-source/quickstart.md). Its MCP server has [ten tools](https://docs.graphify.com/open-source/features/mcp-tools.md) with different names from the hosted ones. |

Before you change a config file, tell the user what you will change and wait for a yes. After you connect, check the connection with `list_repositories`. If anything fails, use [Check your agent is using Graphify](https://docs.graphify.com/platform/verify-connection.md).

## Pick the tool

The hosted server sends instructions on connect that map question types to tools, and it lists 27 tools. Your client builds its tool list from the server, so trust the live tool list and its input schemas over this table.

| The user asks | Call |
| - | - |
| Which repositories or workspaces can I query? | `list_repositories`, `list_workspaces` |
| How does X work? | `query_graph` |
| Where is X defined? | `graphify_find`, or `graphify_node` for the body and its neighbors |
| Find a definition by part of its name, then read it | `search`, then `fetch` with a result's `id` |
| Who calls X? What does X call? | `graphify_callers`, `graphify_callees` |
| How does A reach B? | `graphify_trace` for a directed call path, `shortest_path` for any connection |
| What could break if I change X? | `graphify_impact` for the directly connected callers and callees, then `impact_and_risk` to rank the files by linked tests |
| Where is X used, other than calls? | `graphify_references` |
| Which tests cover X? | `graphify_tests_for` |
| What does this file import, and what imports it? | `graphify_file_neighbors`, or `graphify_imports_exports` for its import and export edges |
| Is the repository indexed, and how fresh is it? | `graph_stats` |
| Which files matter for this task? | `graphify_rank_files` |
| What did the team decide about X? | `recall`, `memories_about` |

Rules for the results:

* Use a `repository_id` from `list_repositories`: the UUID or the `owner/name`. Never invent an ID or silently pick a different repository.
* Check the returned symbol and file before you cite them. If a name matches several symbols, the result lists them under `ambiguous`. Say which one you used. If a name doesn't resolve, you get an error with similar `candidates`, or a `semantic` match instead of an `exact` one. Say so and don't treat it as the symbol the user asked about.
* Results carry `freshness`: the indexed commit and its age. Mention it when the age matters.
* An empty caller list means the index returned no callers. It does not prove the symbol is unused.
* `search` and `graphify_find` match part of a symbol's name, like `ReaSource` or `webhook`, not a question. If a fragment returns nothing, try another name or ask `query_graph` in a full sentence.
* If `graphify_trace` finds no directed call path, it says so and returns the `frontier` it reached. Dynamic calls can hide a real path, so check the callees from there before you say A never reaches B.
* An empty `recall` result means nothing is remembered for that repository yet.
* Impact and test tools read the graph. They don't run tests or prove runtime behavior.
* Use grep for exact strings, such as error messages or config keys.
* If a Graphify tool fails or the repository isn't indexed, say so, then fall back to reading files. Don't guess.

## Ask before you change state

The tools don't edit source files, but two of them change stored state on purpose. Ask the user first:

* `remember` saves a note to the workspace's shared [Memory](https://docs.graphify.com/platform/memory.md). Save only what the user asked you to save.
* `set_workspace` changes which workspace, and so which repositories, the session reads. With `make_default`, it also changes the user's default. See [Hosted MCP](https://docs.graphify.com/platform/hosted-mcp.md#workspaces-and-mcp-sessions).

In workspaces with trail capture turned on, `search`, `query_graph`, `graphify_find`, `graphify_trace`, `graphify_rank_files` and an unscoped `recall` can also save the question you asked to workspace memory. They never change source code.

## Keep answers fresh

Hosted Graphify serves the indexed graph of each repository's default branch. A push to the default branch starts a new index. Other branches and uncommitted changes are not in the graph. See [Repository indexing and sync](https://docs.graphify.com/platform/repositories.md).

* Before you edit, read the local files the graph pointed you to. The checkout can be ahead of the index.
* If the user's change is on a feature branch, say that the graph reflects the default branch.
* If a repository shows **Out of date**, tell the user. A reindex in the Console refreshes it.

With Graphify CLI, the graph is a file on the machine. Run `graphify update .` after a pull or merge, or offer `graphify hook install` to refresh after each commit. See [Incremental updates](https://docs.graphify.com/open-source/features/incremental-updates.md).

## While sign-in is pending

You can add the server, but only the user can finish the OAuth sign-in in a browser. Until they do, every tool call fails and the client shows the server as needing login.

1. Don't retry in a loop, and don't switch to Graphify CLI unless the user asks.
2. Tell the user exactly what to do for their client: for example `/mcp` → **graphify** → **Authenticate** in Claude Code, or `codex mcp login graphify` in Codex. The full list is in [Check your agent is using Graphify](https://docs.graphify.com/platform/verify-connection.md).
3. Remind them that a new server loads only when a session starts, so they may need to reload the editor or start a new session.
4. Meanwhile, answer from the local files and say that the answer did not come from Graphify.
5. After sign-in, call `list_repositories` and show the result.

If `list_repositories` succeeds but is empty, sign-in worked and no repository is indexed in this workspace. Ask the user to index one at [app.graphify.com](https://app.graphify.com) or switch workspace.

## Related

> [card] [Setup for AI agents](https://docs.graphify.com/for-agents.md#setup-for-ai-agents)
>
> The step-by-step setup to follow for a user.

> [card] [Check your agent is using Graphify](https://docs.graphify.com/platform/verify-connection.md)
>
> Test prompts and fixes per client.

> [card] [Hosted MCP](https://docs.graphify.com/platform/hosted-mcp.md)
>
> Sign-in, workspaces, limits and errors.

> [card] [Make agents use the graph](https://docs.graphify.com/cookbooks/make-agents-use-the-graph.md)
>
> Rules and hooks so the agent picks Graphify before grep.


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