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server for semantic search of GitHub issues/PRs via Cloudflare Worker","maintainers":[{"name":"liplus-language","email":"smileygames2021@gmail.com"}],"readme":"# github-rag-mcp\n\nStdio MCP proxy that bridges local MCP clients (Claude Desktop, Claude Code, etc.) to a remote [github-rag-mcp](https://github.com/Liplus-Project/github-rag-mcp) Cloudflare Worker for semantic and structured search over GitHub issues, pull requests, releases, documentation, GitHub Wiki pages, commit diffs, and comment / review surfaces (issue/PR top-level comments, PR review bodies, PR inline review comments).\n\nThis package is the **client-side proxy only**. The actual indexing pipeline (Vectorize + D1 FTS5 + Workers AI BGE-M3 + cross-encoder rerank) runs on the Worker. See the [main repository](https://github.com/Liplus-Project/github-rag-mcp) for architecture and self-hosting instructions.\n\n## Breaking change: MCP protocol revision 2026-07-28\n\nFrom this release the Worker serves **MCP protocol revision 2026-07-28 only**, with no compatibility lane for the previous revision.\n\n- **Proxy versions older than this release stop working.** They open a session with `initialize`, which the Worker no longer answers. The failure is quiet: the proxy does not crash, it returns the protocol error as tool output text.\n- **Restart Claude Desktop to pick up the new proxy.** `npx` resolves `@latest` at process start, so an already-running Claude Desktop keeps the copy it launched with however new the published version is. Quit it fully and reopen.\n- **Pinning the proxy version leaves you stuck.** If your MCP client config pins a version older than this release, restarting does not help; remove the pin (or move it forward) first.\n\nNothing else changes for you: the proxy still speaks the same MCP dialect to Claude Desktop, and the same `search` tool with the same parameters.\n\n## What this proxy does\n\n- Speaks stdio MCP locally to your client (SDK v1, unchanged by the revision above).\n- Forwards `tools/call` to the Worker's `/mcp` endpoint over MCP protocol revision 2026-07-28. That side is stateless: no `initialize` handshake and no session id — each call carries the revision's per-request envelope.\n- Handles OAuth 2.1 with PKCE against the Worker (browser-based localhost callback).\n- Caches access and refresh tokens under `~/.github-rag-mcp/` (mode `0600`).\n\n## Requirements\n\n- Node.js >= 18\n- A reachable github-rag-mcp Worker (the public default is `https://github-rag-mcp.liplus.workers.dev`; you can also point at your own deployment)\n- A web browser on the same machine (used once for OAuth authorization)\n\n## Install / Run\n\nThe proxy is published to npm and exposes a `github-rag-mcp` binary.\n\nRun directly with `npx` (no global install required):\n\n```bash\nnpx github-rag-mcp\n```\n\nOr install globally:\n\n```bash\nnpm install -g github-rag-mcp\ngithub-rag-mcp\n```\n\nThe first run opens a browser window to complete OAuth against the Worker. After authorization, tokens are stored under `~/.github-rag-mcp/` and refreshed automatically.\n\n## Client configuration\n\n### Claude Desktop / Claude Code\n\nAdd the server to your MCP client configuration. Example for Claude Desktop (`claude_desktop_config.json`):\n\n```json\n{\n  \"mcpServers\": {\n    \"github-rag\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"github-rag-mcp\"],\n      \"alwaysLoad\": true\n    }\n  }\n}\n```\n\nTo target a self-hosted Worker, set the `RAG_WORKER_URL` environment variable:\n\n```json\n{\n  \"mcpServers\": {\n    \"github-rag\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"github-rag-mcp\"],\n      \"env\": {\n        \"RAG_WORKER_URL\": \"https://your-worker.example.workers.dev\"\n      },\n      \"alwaysLoad\": true\n    }\n  }\n}\n```\n\n> **Note on `alwaysLoad`:** Recognized by Claude Code v2.1.121+ (released 2026-04-28). When set, the client loads this server's tools at session start instead of deferring them behind a `ToolSearch` round-trip — useful for retrieval servers used on every turn. Older clients (such as Claude Desktop) silently ignore the field, so it is safe to leave in place.\n\n## Configuration\n\n| Variable | Required | Default | Description |\n|---|---|---|---|\n| `RAG_WORKER_URL` | No | `https://github-rag-mcp.liplus.workers.dev` | Base URL of the Cloudflare Worker that exposes the MCP endpoint and OAuth metadata. |\n\nOAuth client registration and tokens are stored in:\n\n- `~/.github-rag-mcp/oauth-client.json` (dynamic client registration)\n- `~/.github-rag-mcp/oauth-tokens.json` (access + refresh tokens)\n\nThe proxy reuses a cached client registration only when it includes every\nredirect URI required by the current localhost callback listener. Because the\nlistener uses a random port, a registration from a previous authorization may\nbe replaced automatically before the browser opens.\n\nDelete these files to force a fresh authorization flow.\n\n## Tools exposed\n\n`search` covers every retrieval mode, alongside private `memory_history`, `record_source_use`, and `record_outcome` tools. Earlier builds split these across `get_issue_context`, `get_doc_content`, and `list_recent_activity`; those tools have been removed and their use cases now fold into the parameters of `search`.\n\n| Tool | Description |\n|---|---|\n| `search` | Unified search across GitHub issues, pull requests, releases, repository documentation, **GitHub Wiki pages**, commit diffs, and comment / review surfaces. Four modes are selected by the parameter set: (1) **hybrid semantic search** — dense BGE-M3 over Vectorize + sparse BM25 over D1 FTS5, fused via RRF, then re-scored with the `bge-reranker-base` cross-encoder; (2) **time-ordered activity scan** — leave `query` empty and set `sort` to `updated_desc` / `created_desc`, optionally narrowed with `since` / `until`; (3) **doc / wiki content fetch** — set `include_content: true` to inline raw markup on top `doc` and `wiki_doc` rows; (4) **stored-content fetch** — pass `vector_ids` (the `vector_id` values carried by earlier results) to read back the body text the index holds for those exact rows, for every type and with no GitHub API call. That text is the indexed copy, truncated at the 8000-character ingest ceiling, so each row carries `content_truncated`; unknown ids land in `not_found` and the rest still return. Structured filters (`repo`, `state`, `labels`, `milestone`, `assignee`, `type`, `top_k`, `fusion`, `rerank`) apply in every mode except stored-content fetch, where the rows are named rather than selected. Search mode also accepts an opt-in `graph_expand` (with `graph_hops`, 1 or 2) that performs a GraphRAG expansion over the Decision-Structure mention graph and appends related wiki entries; it is off by default. |\n\nThe `type` filter accepts: `issue`, `pull_request`, `release`, `doc`, `wiki_doc`, `diff`, `issue_comment`, `pr_review`, `pr_review_comment`, or `all` (default).\n\n`search` writes private retrieval history and has `readOnlyHint:false`. The three feedback tools provide bounded history, explicit selected/validated/used records, and confirmed path reinforcement with receipt-based correction/rollback. `use_memory` defaults false and only changes same-hop graph ordering. Include `server/search-schema.json` and `server/memory-tools.json` in shipped artifacts. See the [memory specification](https://github.com/Liplus-Project/github-rag-mcp/blob/main/docs/2-feedback-memory.md) for bounds, costs, migration 0008-before-deployment and the synthetic lifecycle. For the full parameter reference and examples, see the [main repository README](https://github.com/Liplus-Project/github-rag-mcp#search).\n\n## Authentication flow\n\n1. On first tool call, the proxy discovers OAuth metadata at `${RAG_WORKER_URL}/.well-known/oauth-authorization-server`.\n2. It performs Dynamic Client Registration (RFC 7591) if no compatible client\n   is cached for the current localhost callback URIs.\n3. It starts a one-shot localhost HTTP listener on a random port and opens the browser to the Worker's authorization endpoint.\n4. After you approve, the Worker redirects to `http://127.0.0.1:<port>/callback` with an authorization code.\n5. The proxy exchanges the code for tokens (PKCE S256) and saves them before the\n   browser shows success. Exchange or storage failures show an authorization failure.\n6. Subsequent calls read shared token storage, including another process's updates,\n   and silently refresh when the token nears expiry. A `401` rejects the bearer\n   actually sent, including the transport's final retry. Rejected access tokens and\n   failed refresh credentials are excluded in that process; a fresh token from disk\n   can still be used. New records retain the issuing client ID for refresh; older\n   records use the shared client registration as a fallback.\n\nWhile authorization is pending, tool calls return an authentication requirement\nafter a short wait. Retry after completing the browser flow: the running proxy\nuses the saved tokens. A failed flow or five-minute timeout is reported on a later\ncall; retry again to start a new flow. Concurrent calls share one browser attempt.\n\nThe browser callback never leaves your machine; the authorization code is delivered directly to the local listener.\n\n## Troubleshooting\n\n- **Browser does not open.** Check that your system has a working default browser.\n  The proxy does not log authorization URLs or credentials.\n- **`redirect_uri is not associated with this application`.** Upgrade the\n  proxy. Current versions replace cached client registrations whose redirect\n  URI set does not cover the callback port selected for this authorization.\n- **`OAuth callback timed out after 5 minutes`.** Retry the tool to start a new flow.\n- **`Failed to reach worker`.** Check that `RAG_WORKER_URL` is correct and reachable from your machine.\n- **`Unsupported protocol version`, or a tool that answers with a protocol error instead of results.** The proxy predates the 2026-07-28 flip. Quit Claude Desktop fully and reopen so `npx` fetches the current version; if your config pins a version, move the pin forward first.\n- **Authentication required after authorizing.** Retry the tool after the browser\n  confirms success. The running proxy reads the newly saved token; restarting or\n  deleting credentials is not required for this recovery. A browser failure page\n  means exchange or storage did not complete successfully.\n\n## Links\n\n- Source and architecture: <https://github.com/Liplus-Project/github-rag-mcp>\n- Self-hosting the Worker: [docs/installation.md](https://github.com/Liplus-Project/github-rag-mcp/blob/main/docs/installation.md)\n- Requirements spec: [docs/0-requirements.md](https://github.com/Liplus-Project/github-rag-mcp/blob/main/docs/0-requirements.md)\n- Issue tracker: <https://github.com/Liplus-Project/github-rag-mcp/issues>\n\n## License\n\nApache-2.0. See the [LICENSE](https://github.com/Liplus-Project/github-rag-mcp/blob/main/LICENSE) and [NOTICE](https://github.com/Liplus-Project/github-rag-mcp/blob/main/NOTICE) files in the main repository.\n\nLive inline doc/wiki bodies carry `github_live` provenance and a SHA-256 content version; stored fetch and graph bodies retain indexed-snapshot provenance. The source IDs distinguish those versions without archiving the live body.\n","readmeFilename":"README.md"}