> ## 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
> The PyPI package is graphifyy, with two y's. The command is graphify.
> /graphify . is typed in an assistant chat, not in a shell.
> Use only commands, flags, and endpoints shown on these pages. Do not invent one.
> Choose the surface before you open a page. Local (Graphify Local) is the graphifyy package on the machine: the skill, the CLI, and the ten-tool MCP. Its pages are the Open Source tab (/open-source/) and the Graphify Local tab on each Integrations page. Graphify is the hosted workspace and https://api.graphify.com/mcp (Streamable HTTP, OAuth, no API key). Its pages are the Graphify tab (/platform/, /concepts/) and the Graphify (hosted) tab on each Integrations page. Recommend Graphify (hosted) by default; it needs no local build. Recommend Graphify Local only when the user asks for an offline, on-machine, or self-hosted setup. Cookbooks (/cookbooks/) and /mcp/docs-search apply to both. Each page's source frontmatter records this as surface: local, cloud, or both. Buildkite is the CI integration.
> In llms.txt, tell the surface from the page path. Graphify: /platform/ and /concepts/. Local: /open-source/. Most /integrations/ pages cover both, with a Graphify (hosted) tab and a Graphify Local tab. Everything else applies to both.
> graphifyy release notes are published at https://github.com/Graphify-Labs/graphify/releases and https://graphify.com/changelog. The current package version is on PyPI (https://pypi.org/project/graphifyy/).
> The official site is https://graphify.com. These docs are https://docs.graphify.com.
> The local MCP server is the ten tools in the MCP tool reference and reads a graph on the machine. The hosted server is https://api.graphify.com/mcp (Streamable HTTP, OAuth, no API key). The JetBrains, ChatGPT, Codex, and Dots, and Vercel pages use the hosted server, not the ten-tool list. On pages with tabs, the Graphify (hosted) tab uses the hosted server and the Graphify Local tab uses the local skill or the ten-tool server.
> Read https://docs.graphify.com/llms.txt, then open one page's .md link. Use https://docs.graphify.com/llms-full.txt only when one page is not enough.
> To set up Graphify for a user, follow https://docs.graphify.com/for-agents.md#setup-for-ai-agents.

# Graphify troubleshooting: MCP, 429, and error codes

> Fix MCP OAuth errors, 429 rate_limited, indexing and reindex failures, query and Ask error codes, and GitHub or GitLab connection issues.

This page covers Graphify, the hosted product at [app.graphify.com](https://app.graphify.com). Each section heading uses the error text you see, so you can search for it.

Every API error has the same shape. Include the `correlationId` when you contact support:

```json Error response theme={"theme":{"light":"github-light-default","dark":"github-dark-default"}}
{
  "error": { "code": "rate_limited", "message": "Too many requests. Please slow down." },
  "meta": { "correlationId": "…" }
}
```

## Sign-in and MCP OAuth errors

### MCP client shows "Needs login" or "needs authentication"

Your client hasn't finished the one-time browser sign-in. Graphify answers a request with no token with `401` and a `WWW-Authenticate` header, which starts the sign-in.

* Claude Code: run `/mcp`, select **graphify**, and choose **Authenticate**.
* Codex: run `codex mcp login graphify`.
* Cursor: select **Needs login** next to the server.

See [Hosted MCP](https://docs.graphify.com/platform/hosted-mcp.md#how-hosted-mcp-sign-in-works) for how sign-in works.

### invalid\_grant: "Refresh token superseded; retry the login."

Several agent sessions shared one stored login and refreshed at the same time. Only one refresh wins. Sign in again from the client that failed.

### invalid\_grant: "Refresh token reuse detected." or "Refresh token expired."

The stored login is no longer valid. Sign out of the server in your client, then sign in again. Other `invalid_grant` messages, such as "Authorization code expired." or "PKCE verification failed.", also mean you should start the sign-in again.

### invalid\_client\_metadata: "Only public clients (auth method 'none') are supported."

Your client tried to register with a client secret. Graphify supports public OAuth clients only. Use the client's standard remote MCP setup, or the [`mcp-remote` bridge](https://docs.graphify.com/platform/hosted-mcp#clients-without-remote-oauth).

### 429 on sign-in

Too many token refreshes for one login in a minute. The response includes `Retry-After`. Wait that long, then retry.

### "Your session expired. Signing you back in…"

The console's session ended. The console signs you in again on its own. If it keeps happening, sign out and sign in again.

## MCP workspace errors

### no\_workspace: "No workspace is selected for this agent."

You belong to more than one workspace and haven't picked one. The message lists your workspaces. Ask your agent to run `set_workspace` with one handle. `set_workspace` changes which workspace the session reads from.

### workspace\_access\_revoked

You were removed from the bound workspace, or lost access. Run `list_workspaces` and pick another.

### mcp\_session\_required: "set\_workspace can only run inside an established MCP session."

Reconnect the server in your client, then run `set_workspace` again.

### list\_repositories is empty

You're in a workspace with no indexed repositories, or the repository is still indexing. Check the workspace with `list_workspaces`, and check indexing in the console.

## 429 rate\_limited: "Too many requests. Please slow down."

You went over a default per-minute limit:

| Operation | Default limit |
| - | - |
| Ask | 30/minute per workspace |
| Query | 120/minute per workspace |
| Hosted MCP | 240/minute per client IP |
| Test impact | 60/minute per workspace |

Back off and retry with exponential delay and jitter. The usual cause is an agent calling Graphify in a tight loop. In CI, treat a `429` from test impact as "run the full suite". See [Rate limits](https://docs.graphify.com/platform/support/rate-limits.md).

## Indexing failed or stuck

### "Taking longer than usual. Still indexing."

Large repositories take longer. The build is still running. Wait, and keep using the last published graph in the meantime.

### "Indexing failed"

Open the repository in the console and select **Retry indexing**. For a combined graph, the message is "Your graph couldn’t finish building" with a **Retry build** button.

### "Nothing to show yet"

No code was found in the graph. Select **Reindex repository**. If the repository has no commits on its default branch, GitLab sync reports `repository_empty`: "This repository has no commits on its default branch yet." Push a commit first.

### Plan limits stop a build

Messages such as **Monthly indexing allowance used** or **Daily build limit reached** mean a plan limit, not a fault. See [Rate limits and plan limits](https://docs.graphify.com/platform/support/rate-limits.md#other-limit-responses).

If a build stays stuck, use **Get in touch** under **Settings** in the console.

## Query, Ask, and reindex errors

| Code | Status | Fix |
| - | - | - |
| `repository_required` | 422 | Name a repository in the query. |
| `query_repository_ambiguous` | 422 | Use the full repository name or ID. |
| `query_timeout` | 504 | Over 45 seconds. Narrow the query. |
| `query_busy`, `query_unavailable` | 503 | Retry after the `Retry-After` header. |
| `question_required` | 422 | Ask got an empty question. |
| `ask_unavailable` | 503 | "Ask is not available yet." |
| `index_rebuild_debounced` | 409 | Wait `retryAfterSeconds`, then reindex. |
| `repository_disabled` | 409 | Turn **Indexing** on for the repository. |
| `provider_disconnected` | 409 | Reconnect GitHub or GitLab, or remove the repository. |
| `subscription_required` | 402 | Reactivate the plan in **Billing**. |

Per-workspace limits: Ask 30, query 120, and test impact 60 requests a minute. The hosted MCP allows 240 a minute per client IP. See [Rate limits](https://docs.graphify.com/platform/support/rate-limits.md).

## Repository connect issues

### GitHub repositories are missing

On the **Repositories** page, select **Add GitHub repositories**. It opens GitHub, where you choose which repositories the Graphify app can access. A repository you didn't grant there won't appear. See [GitHub](https://docs.graphify.com/integrations/github.md).

### GitLab: "GitLab is not connected." or "Reconnect GitLab to continue."

Graphify supports GitLab on **gitlab.com only**. Self-managed GitLab isn't supported. Open **Integrations**, then select **Connect** on the GitLab card. If you see `gitlab_reconnect_required`, connect again.

Other GitLab errors:

| Code | Message | What to do |
| - | - | - |
| `gitlab_repository_unavailable` | "GitLab repository access is unavailable." | Check that your GitLab account can still see the project, then reconnect. |
| `gitlab_sync_conflict` | "The GitLab connection changed while syncing. Retry the sync." | Retry the sync. |
| `repository_empty` | "This repository has no commits on its default branch yet." | Push a commit. |

See [GitLab](https://docs.graphify.com/integrations/gitlab.md).

## MCP client config mistakes

| Mistake | Fix |
| - | - |
| VS Code config uses `mcpServers` | VS Code uses `servers`. |
| Gemini CLI config uses `url` | Gemini CLI uses `httpUrl` for remote servers. |
| Copilot CLI connects but has no tools | Add `"tools": ["*"]` to `~/.copilot/mcp-config.json`. |
| A token or API key pasted into the config | Remove it. The hosted server signs in with OAuth. |
| Wrong URL | Use `https://api.graphify.com/mcp`. |
| `npx` not found with `mcp-remote` | Install Node.js where the client can find it, or use native remote setup. |
| `413 mcp_body_too_large` | A request body was over 256 KB. Send smaller requests. |

Per-client setup is in [Integrations](https://docs.graphify.com/integrations/overview.md).

## Graphify vs Graphify Local confusion

| Symptom | Cause |
| - | - |
| The agent doesn't see uncommitted changes | The hosted MCP serves the indexed graph. Use the [local MCP server](https://docs.graphify.com/open-source/mcp-server.md) for local work. |
| A Local command or flag doesn't work in the console | Graphify Local is the open-source CLI. It's a separate product. |
| Rate limits on Local | Graphify Local runs on your machine and has no rate limits. |
| Moving a Local graph to Graphify | See [Move from Local](https://docs.graphify.com/platform/support/move-from-local.md). |

See [Graphify vs Graphify Local](https://docs.graphify.com/platform/graphify-vs-local.md).

## Still stuck

> **[FAQs](https://docs.graphify.com/platform/support/faqs.md)**
>
> Common questions.

> **[Hosted MCP](https://docs.graphify.com/platform/hosted-mcp.md)**
>
> Setup and verification.


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