mne-docs-mcp 1.0.22 → 1.0.23

package/README.md

@@ -18,7 +18,7 @@ $env:MNE_GITHUB_TOKEN="ghp_your_token_here"   # Windows PowerShell
 npm start
 ```
 
-Server runs on `http://localhost:8000`. Verify with `curl http://localhost:8000/health`.
+Server runs on `http://127.0.0.1:8000` by default. Verify with `curl http://localhost:8000/health`.
 
 > **Prerequisites:** Node.js ≥ 20 and Python 3 (used for AST parsing — no pip packages required).
 
@@ -78,7 +78,7 @@ MNE_TRANSPORT=http npm start
 | Endpoint | Description |
 |----------|-------------|
 | `POST /mcp` | MCP protocol (JSON-RPC) |
-| `GET /health` | Health check — returns `{"status":"ok"}` |
+| `GET /health` | Health check — returns `{"status":"healthy"}` |
 | `GET /metrics` | Runtime metrics (request counts, cache hit rate, GitHub rate limit) |
 
 ### Docker
@@ -141,7 +141,9 @@ All tools support a `package` parameter to query across the MNE ecosystem: `mne-
 |----------|-------------|---------|
 | `MNE_GITHUB_TOKEN` | GitHub PAT (**required**) | — |
 | `MNE_PORT` | Server port (HTTP mode) | `8000` |
+| `MNE_HOST` | Bind address (use `0.0.0.0` in Docker) | `127.0.0.1` |
 | `MNE_TRANSPORT` | `http` or `stdio` | `http` |
+| `MNE_ALLOWED_ORIGINS` | Comma-separated origins for CORS (use `*` to allow all) | `*` |
 | `MNE_DEFAULT_PACKAGE` | Default MNE package | `mne-python` |
 | `MNE_PYTHON_PATH` | Python executable path | `python` (Win) / `python3` (Unix) |
 | `MNE_LOG_LEVEL` | `debug` / `info` / `warn` / `error` | `info` |
@@ -154,18 +156,20 @@ See `.env.example` for advanced options: cache TTLs (`MNE_CACHE_TTL_MINUTES`, `M
 ```
 ┌─────────────────────────────────────────────────────────┐
 │  TypeScript Server (Node.js)                            │
-│  ├─ MCP Tools (McpServer API, SDK v1.18+)              │
-│  ├─ GitHub Client (rate limiting, caching)             │
+│  ├─ MCP Tools (McpServer API, SDK v1.18+)               │
+│  │  · Tool annotations (readOnly, idempotent, etc.)     │
+│  │  · Structured output + resource_link content        │
+│  ├─ GitHub Client (rate limiting, caching)              │
 │  └─ Python Parser Bridge ──┐                            │
 └────────────────────────────┼────────────────────────────┘
                              ▼
                     ┌─────────────────┐
-                    │  Python Parser  │
+                    │  Python Parser │
                     │  (AST, stdlib)  │
                     └─────────────────┘
 ```
 
-Built with the official [MCP TypeScript SDK](https://github.com/modelcontextprotocol/typescript-sdk).
+Built with the official [MCP TypeScript SDK](https://github.com/modelcontextprotocol/typescript-sdk). This server conforms to the [Model Context Protocol specification 2025-06-18](https://modelcontextprotocol.io/specification/2025-06-18) (tool annotations, structured output, resource links, Origin validation, Streamable HTTP).
 
 ## Development
 
@@ -236,12 +240,14 @@ OIDC is used for MCP Registry authentication (no extra secret needed).
 
 - **Rate limits:** Ensure `MNE_GITHUB_TOKEN` is set
 - **Parser fails:** Check Python 3 is installed (path auto-detected per platform)
-- **Test setup:** Run `npx tsx examples/mcp-client.ts` to verify (requires dev dependencies — run `npm install` first)
+- **Test setup:** Run `node run-tests.mjs` to verify (requires the server running on `localhost:8000`)
 
 ## Security
 
 - GitHub token needs only `public_repo` scope — never commit tokens to version control
 - Python parser uses `ast.parse()` only (no code execution)
+- HTTP mode validates the `Origin` header when `MNE_ALLOWED_ORIGINS` is set (comma-separated list); use `*` to allow all (default)
+- By default the server binds to `127.0.0.1`; set `MNE_HOST=0.0.0.0` only when needed (e.g. in Docker)
 - For production: restrict outbound to `api.github.com` and `mne.discourse.group`, don't expose to public internet
 
 ## License

package/dist/config.d.ts

@@ -14,13 +14,16 @@ export interface MnePackageInfo {
 export declare const MNE_PACKAGES: Record<string, MnePackageInfo>;
 export declare const MNE_PACKAGE_NAMES: string[];
 export declare const DEFAULT_PACKAGE = "mne-python";
+export declare const packageSchema: z.ZodOptional<z.ZodEnum<[string, ...string[]]>>;
 /**
  * Get package info by name, with fallback to default.
  */
 export declare function getPackageInfo(packageName?: string): MnePackageInfo;
 export declare const ConfigSchema: z.ZodObject<{
     port: z.ZodDefault<z.ZodNumber>;
+    host: z.ZodDefault<z.ZodString>;
     transport: z.ZodDefault<z.ZodEnum<["http", "stdio"]>>;
+    allowedOrigins: z.ZodDefault<z.ZodString>;
     githubToken: z.ZodString;
     githubApiBase: z.ZodDefault<z.ZodString>;
     defaultPackage: z.ZodDefault<z.ZodString>;
@@ -39,7 +42,9 @@ export declare const ConfigSchema: z.ZodObject<{
     logJson: z.ZodDefault<z.ZodBoolean>;
 }, "strip", z.ZodTypeAny, {
     port: number;
+    host: string;
     transport: "http" | "stdio";
+    allowedOrigins: string;
     githubToken: string;
     githubApiBase: string;
     defaultPackage: string;
@@ -59,7 +64,9 @@ export declare const ConfigSchema: z.ZodObject<{
 }, {
     githubToken: string;
     port?: number | undefined;
+    host?: string | undefined;
     transport?: "http" | "stdio" | undefined;
+    allowedOrigins?: string | undefined;
     githubApiBase?: string | undefined;
     defaultPackage?: string | undefined;
     githubTimeout?: number | undefined;

package/dist/config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB;;;GAGG;AACH,MAAM,WAAW,cAAc;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,eAAO,MAAM,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,cAAc,CAmDvD,CAAC;AAEF,eAAO,MAAM,iBAAiB,UAA4B,CAAC;AAC3D,eAAO,MAAM,eAAe,eAAe,CAAC;AAE5C,eAAO,MAAM,aAAa,iDAC4E,CAAC;AAEvG;;GAEG;AACH,wBAAgB,cAAc,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,cAAc,CAOnE;AAED,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqBvB,CAAC;AAEH,MAAM,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,YAAY,CAAC,CAAC;AAElD,wBAAgB,UAAU,IAAI,MAAM,CAsCnC"}

package/dist/config.js

@@ -56,6 +56,8 @@ export const MNE_PACKAGES = {
 };
 export const MNE_PACKAGE_NAMES = Object.keys(MNE_PACKAGES);
 export const DEFAULT_PACKAGE = 'mne-python';
+export const packageSchema = z.enum(MNE_PACKAGE_NAMES).optional()
+    .describe('MNE package to search (default: mne-python). Options: ' + MNE_PACKAGE_NAMES.join(', '));
 /**
  * Get package info by name, with fallback to default.
  */
@@ -69,7 +71,9 @@ export function getPackageInfo(packageName) {
 }
 export const ConfigSchema = z.object({
     port: z.coerce.number().default(8000),
+    host: z.string().default('127.0.0.1'),
     transport: z.enum(['http', 'stdio']).default('http'),
+    allowedOrigins: z.string().default('*'),
     githubToken: z.string().min(1),
     githubApiBase: z.string().default('https://api.github.com'),
     defaultPackage: z.string().default(DEFAULT_PACKAGE),
@@ -90,7 +94,9 @@ export const ConfigSchema = z.object({
 export function loadConfig() {
     const config = {
         port: process.env.MNE_PORT,
+        host: process.env.MNE_HOST,
         transport: process.env.MNE_TRANSPORT,
+        allowedOrigins: process.env.MNE_ALLOWED_ORIGINS,
         githubToken: process.env.MNE_GITHUB_TOKEN,
         githubApiBase: process.env.MNE_GITHUB_API_BASE,
         defaultPackage: process.env.MNE_DEFAULT_PACKAGE,

package/dist/config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAYxB;;GAEG;AACH,MAAM,CAAC,MAAM,YAAY,GAAmC;IACxD,YAAY,EAAE;QACV,IAAI,EAAE,sBAAsB;QAC5B,UAAU,EAAE,MAAM;QAClB,OAAO,EAAE,2BAA2B;KACvC;IACD,mBAAmB,EAAE;QACjB,IAAI,EAAE,6BAA6B;QACnC,UAAU,EAAE,oBAAoB;QAChC,OAAO,EAAE,6CAA6C;KACzD;IACD,UAAU,EAAE;QACR,IAAI,EAAE,oBAAoB;QAC1B,UAAU,EAAE,WAAW;QACvB,OAAO,EAAE,oCAAoC;KAChD;IACD,kBAAkB,EAAE;QAChB,IAAI,EAAE,4BAA4B;QAClC,UAAU,EAAE,mBAAmB;QAC/B,OAAO,EAAE,4CAA4C;KACxD;IACD,UAAU,EAAE;QACR,IAAI,EAAE,oBAAoB;QAC1B,UAAU,EAAE,WAAW;QACvB,OAAO,EAAE,oCAAoC;KAChD;IACD,SAAS,EAAE;QACP,IAAI,EAAE,mBAAmB;QACzB,UAAU,EAAE,UAAU;QACtB,OAAO,EAAE,mCAAmC;KAC/C;IACD,cAAc,EAAE;QACZ,IAAI,EAAE,wBAAwB;QAC9B,UAAU,EAAE,eAAe;QAC3B,OAAO,EAAE,wCAAwC;KACpD;IACD,cAAc,EAAE;QACZ,IAAI,EAAE,wBAAwB;QAC9B,UAAU,EAAE,eAAe;QAC3B,OAAO,EAAE,iCAAiC;KAC7C;IACD,SAAS,EAAE;QACP,IAAI,EAAE,mBAAmB;QACzB,UAAU,EAAE,UAAU;QACtB,OAAO,EAAE,mCAAmC;KAC/C;IACD,gBAAgB,EAAE;QACd,IAAI,EAAE,0BAA0B;QAChC,UAAU,EAAE,iBAAiB;QAC7B,OAAO,EAAE,mCAAmC;KAC/C;CACJ,CAAC;AAEF,MAAM,CAAC,MAAM,iBAAiB,GAAG,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;AAC3D,MAAM,CAAC,MAAM,eAAe,GAAG,YAAY,CAAC;AAE5C,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,CAAC,IAAI,CAAC,iBAA0C,CAAC,CAAC,QAAQ,EAAE;KACrF,QAAQ,CAAC,wDAAwD,GAAG,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;AAEvG;;GAEG;AACH,MAAM,UAAU,cAAc,CAAC,WAAoB;IAC/C,MAAM,IAAI,GAAG,WAAW,IAAI,eAAe,CAAC;IAC5C,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC;IAChC,IAAI,CAAC,IAAI,EAAE,CAAC;QACR,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,gBAAgB,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChG,CAAC;IACD,OAAO,IAAI,CAAC;AAChB,CAAC;AAED,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IACjC,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,WAAW,CAAC;IACrC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC;IACpD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;IACvC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;IAC9B,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,wBAAwB,CAAC;IAC3D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,eAAe,CAAC;IACnD,aAAa,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;IAC/C,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,6BAA6B,CAAC;IAC/D,YAAY,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;IAC9C,sBAAsB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;IACtD,qBAAqB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;IACrD,mBAAmB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC;IAClD,qBAAqB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC;IACpD,oBAAoB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC;IACnD,eAAe,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC;IAChD,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC;IACnF,aAAa,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;IAC/C,QAAQ,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC;IACpE,OAAO,EAAE,CAAC,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;CAC7C,CAAC,CAAC;AAIH,MAAM,UAAU,UAAU;IACtB,MAAM,MAAM,GAAG;QACX,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,QAAQ;QAC1B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,QAAQ;QAC1B,SAAS,EAAE,OAAO,CAAC,GAAG,CAAC,aAAa;QACpC,cAAc,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB;QAC/C,WAAW,EAAE,OAAO,CAAC,GAAG,CAAC,gBAAgB;QACzC,aAAa,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB;QAC9C,cAAc,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB;QAC/C,aAAa,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB;QAC7C,YAAY,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB;QAC5C,YAAY,EAAE,OAAO,CAAC,GAAG,CAAC,iBAAiB;QAC3C,sBAAsB,EAAE,OAAO,CAAC,GAAG,CAAC,qBAAqB;QACzD,qBAAqB,EAAE,OAAO,CAAC,GAAG,CAAC,4BAA4B;QAC/D,mBAAmB,EAAE,OAAO,CAAC,GAAG,CAAC,0BAA0B;QAC3D,qBAAqB,EAAE,OAAO,CAAC,GAAG,CAAC,4BAA4B;QAC/D,oBAAoB,EAAE,OAAO,CAAC,GAAG,CAAC,2BAA2B;QAC7D,eAAe,EAAE,OAAO,CAAC,GAAG,CAAC,qBAAqB;QAClD,UAAU,EAAE,OAAO,CAAC,GAAG,CAAC,eAAe;QACvC,aAAa,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB;QAC7C,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,aAAa;QACnC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,YAAY;KACpC,CAAC;IAEF,wDAAwD;IACxD,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,CAClC,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC,CAC7D,CAAC;IAEF,IAAI,CAAC;QACD,OAAO,YAAY,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC;IAC3C,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACb,IAAI,KAAK,YAAY,CAAC,CAAC,QAAQ,EAAE,CAAC;YAC9B,MAAM,MAAM,GAAG,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACrF,MAAM,IAAI,KAAK,CAAC,qCAAqC,MAAM,wCAAwC,CAAC,CAAC;QACzG,CAAC;QACD,MAAM,KAAK,CAAC;IAChB,CAAC;AACL,CAAC"}

package/dist/index.js

@@ -38,6 +38,34 @@ async function main() {
         app.get('/metrics', (req, res) => {
             res.json(metrics.getMetrics());
         });
+        // CORS and Origin validation (MCP spec: validate Origin to prevent DNS rebinding)
+        const allowedOriginsList = config.allowedOrigins === '*' ? ['*'] : config.allowedOrigins.split(',').map(s => s.trim()).filter(Boolean);
+        app.use('/mcp', (req, res, next) => {
+            const origin = req.headers.origin;
+            if (origin) {
+                if (allowedOriginsList.includes('*')) {
+                    res.setHeader('Access-Control-Allow-Origin', '*');
+                }
+                else if (allowedOriginsList.includes(origin)) {
+                    res.setHeader('Access-Control-Allow-Origin', origin);
+                }
+                else {
+                    res.status(403).json({ error: 'Origin not allowed' });
+                    return;
+                }
+            }
+            else {
+                res.setHeader('Access-Control-Allow-Origin', '*');
+            }
+            res.setHeader('Access-Control-Allow-Methods', 'GET, POST, DELETE, OPTIONS');
+            res.setHeader('Access-Control-Allow-Headers', 'Content-Type, Accept, Mcp-Session-Id');
+            res.setHeader('Access-Control-Expose-Headers', 'Mcp-Session-Id');
+            if (req.method === 'OPTIONS') {
+                res.status(204).end();
+                return;
+            }
+            next();
+        });
         // Session management for Streamable HTTP
         const sessions = new Map();
         // Streamable HTTP endpoint - handles POST, GET, DELETE
@@ -89,9 +117,9 @@ async function main() {
                 res.status(405).json({ error: 'Method not allowed' });
             }
         });
-        app.listen(config.port, () => {
-            logger.info(`Server listening on port ${config.port}`);
-            logger.info(`MCP endpoint: http://localhost:${config.port}/mcp`);
+        app.listen(config.port, config.host, () => {
+            logger.info(`Server listening on ${config.host}:${config.port}`);
+            logger.info(`MCP endpoint: http://${config.host === '0.0.0.0' ? 'localhost' : config.host}:${config.port}/mcp`);
         });
     }
     else {

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/server.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,EAAE,MAAM,EAAqB,MAAM,aAAa,CAAC;AA6BxD,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,sBA8QhD"}
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAgDrC,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,sBAwDhD"}

package/dist/server.js

@@ -1,60 +1,79 @@
 import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
-import { z } from 'zod';
-import { MNE_PACKAGE_NAMES } from './config.js';
 import { getLogger } from './utils/logger.js';
 import { metrics } from './utils/metrics.js';
 import { GitHubClient } from './github/client.js';
 import { CacheManager } from './cache/manager.js';
-import { listMneVersions } from './tools/listMneVersions.js';
-import { getMneFile } from './tools/getMneFile.js';
-import { getMneDoc } from './tools/getMneDoc.js';
-import { findMneSymbol } from './tools/findMneSymbol.js';
-import { searchMneDocs } from './tools/searchMneDocs.js';
-import { searchMneIssues } from './tools/searchMneIssues.js';
-import { getMneIssue } from './tools/getMneIssue.js';
-import { getMneIssueComments } from './tools/getMneIssueComments.js';
-import { searchMneForum } from './tools/searchMneForum.js';
-import { getSymbolReferences } from './tools/getSymbolReferences.js';
-import { getMneForumTopic } from './tools/getMneForumTopic.js';
-import { getMneChangelog } from './tools/getMneChangelog.js';
-import { getMneExample } from './tools/getMneExample.js';
-import { getRelatedSymbols } from './tools/getRelatedSymbols.js';
-import { lookupMneError } from './tools/lookupMneError.js';
 import { PythonParserBridge } from './parser/bridge.js';
 import { ForumClient } from './forum/client.js';
 import { McpError } from './types.js';
 import { getVersion } from './version.js';
-// Zod schema for package parameter
-const packageSchema = z.enum(MNE_PACKAGE_NAMES).optional()
-    .describe('MNE package to search (default: mne-python). Options: ' + MNE_PACKAGE_NAMES.join(', '));
+import * as allTools from './tools/index.js';
+const URL_KEYS = ['sourceUrl', 'docsUrl', 'htmlUrl', 'url'];
+const RESOURCE_LINK_NAMES = { sourceUrl: 'Source', docsUrl: 'Docs', htmlUrl: 'Link', url: 'Link' };
+function isHttpUrl(s) {
+    return typeof s === 'string' && (s.startsWith('http://') || s.startsWith('https://'));
+}
+function extractResourceLinks(result) {
+    const seen = new Set();
+    const links = [];
+    function collect(obj) {
+        if (!obj || typeof obj !== 'object')
+            return;
+        if (Array.isArray(obj)) {
+            obj.forEach(collect);
+            return;
+        }
+        for (const key of URL_KEYS) {
+            const val = obj[key];
+            if (isHttpUrl(val) && !seen.has(val)) {
+                seen.add(val);
+                links.push({
+                    type: 'resource_link',
+                    uri: val,
+                    name: RESOURCE_LINK_NAMES[key] ?? 'Link',
+                    annotations: { audience: ['user', 'assistant'], priority: 0.9 },
+                });
+            }
+        }
+        for (const v of Object.values(obj)) {
+            if (Array.isArray(v))
+                v.forEach(collect);
+            else if (v && typeof v === 'object')
+                collect(v);
+        }
+    }
+    collect(result);
+    return links;
+}
 export async function createServer(config) {
     const logger = getLogger();
     logger.info('Initializing MNE Docs MCP Server...');
-    // Initialize components
-    const githubClient = new GitHubClient(config);
-    const cacheManager = new CacheManager(config);
-    const parserBridge = new PythonParserBridge(config);
-    const forumClient = new ForumClient(config.forumBaseUrl, config.forumTimeout);
-    // Tool context
     const toolContext = {
-        github: githubClient,
-        cache: cacheManager,
-        parser: parserBridge,
-        forum: forumClient,
+        github: new GitHubClient(config),
+        cache: new CacheManager(config),
+        parser: new PythonParserBridge(config),
+        forum: new ForumClient(config.forumBaseUrl, config.forumTimeout),
     };
     const server = new McpServer({
         name: 'mne-docs-mcp',
         version: getVersion(),
     });
-    // Helper to wrap tool execution with logging and metrics
-    const wrapTool = (name, handler) => {
-        return async (args) => {
+    for (const tool of Object.values(allTools)) {
+        const { name, title, description, inputSchema, annotations, outputSchema } = tool.definition;
+        server.registerTool(name, { title, description, inputSchema, ...(annotations && { annotations }), ...(outputSchema && { outputSchema }) }, async (args) => {
             logger.info(`Tool call: ${name}`, args);
             metrics.recordToolCall(name);
             try {
-                const result = await handler(args);
+                const result = await tool.handler(args, toolContext);
                 const text = typeof result === 'string' ? result : JSON.stringify(result, null, 2);
-                return { content: [{ type: 'text', text }] };
+                const content = [
+                    { type: 'text', text, annotations: { audience: ['assistant'], priority: 1 } },
+                    ...(typeof result === 'object' && result !== null ? extractResourceLinks(result) : []),
+                ];
+                if (outputSchema && typeof result === 'object' && result !== null) {
+                    return { content, structuredContent: result };
+                }
+                return { content };
             }
             catch (error) {
                 if (error instanceof McpError) {
@@ -71,152 +90,8 @@ export async function createServer(config) {
                     isError: true,
                 };
             }
-        };
-    };
-    // Register tools
-    server.registerTool('list_mne_versions', {
-        title: 'List MNE Versions',
-        description: 'List available release versions for MNE-Python or related packages (mne-bids, mne-connectivity, etc.). Use to find valid version numbers before querying docs or code.',
-        inputSchema: {
-            limit: z.number().optional().describe('Max versions to return (default: 20)'),
-            stableOnly: z.boolean().optional().describe('Only return stable releases, excluding alpha/beta/rc/dev tags (default: false)'),
-            package: packageSchema,
-        },
-    }, wrapTool('list_mne_versions', (args) => listMneVersions(args, toolContext)));
-    server.registerTool('get_mne_file', {
-        title: 'Get MNE File',
-        description: 'Fetch raw source code from MNE-Python or related package repositories. Use when you need to see the actual implementation of a function or class.',
-        inputSchema: {
-            path: z.string().describe('File path in repo, e.g. "mne/epochs.py" or "mne_bids/write.py"'),
-            version: z.string().optional().describe('Version tag, e.g. "1.6.0" (default: latest)'),
-            maxLines: z.number().optional().describe('Truncate output to N lines'),
-            startLine: z.number().optional().describe('Start from this line number'),
-            endLine: z.number().optional().describe('End at this line number'),
-            package: packageSchema,
-        },
-    }, wrapTool('get_mne_file', (args) => getMneFile(args, toolContext)));
-    server.registerTool('get_mne_doc', {
-        title: 'Get MNE Documentation',
-        description: 'Get the docstring and API documentation for an MNE-Python class, function, or method. Returns signature, parameters, examples, and links to official docs. Use when users ask "how do I use X?" or "what does X do?"',
-        inputSchema: {
-            symbol: z.string().describe('Fully qualified name, e.g. "mne.Epochs", "mne.io.read_raw_fif", "mne.preprocessing.ICA"'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            brief: z.boolean().optional().describe('Return only summary and signature to save tokens (default: false)'),
-        },
-    }, wrapTool('get_mne_doc', (args) => getMneDoc(args, toolContext)));
-    server.registerTool('find_mne_symbol', {
-        title: 'Find MNE Symbol',
-        description: 'Search for classes, functions, or methods in MNE-Python by name. Use when you know part of a name but not the full path, e.g. "filter" finds mne.filter.filter_data, mne.io.Raw.filter, etc.',
-        inputSchema: {
-            query: z.string().describe('Search term, e.g. "filter", "epoch", "ica"'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            maxResults: z.number().optional().describe('Max results to return (default: 10)'),
-            includePrivate: z.boolean().optional().describe('Include private (_name) symbols (default: false)'),
-        },
-    }, wrapTool('find_mne_symbol', (args) => findMneSymbol(args, toolContext)));
-    server.registerTool('search_mne_docs', {
-        title: 'Search MNE Docs',
-        description: 'Full-text search across MNE documentation, source code, GitHub issues, and community forum. Use for broad queries like "how to remove artifacts" or "memory error when loading".',
-        inputSchema: {
-            query: z.string().describe('Search query, e.g. "artifact rejection", "ICA tutorial", "memory leak"'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            maxResultsPerSource: z.number().optional().describe('Max results per source type (default: 5)'),
-            package: packageSchema,
-        },
-    }, wrapTool('search_mne_docs', (args) => searchMneDocs(args, toolContext)));
-    server.registerTool('search_mne_issues', {
-        title: 'Search MNE Issues',
-        description: 'Search GitHub issues for MNE packages. Use to find bug reports, feature requests, or known problems. Helpful when users encounter errors or unexpected behavior.',
-        inputSchema: {
-            query: z.string().describe('Search query, e.g. "memory leak", "segmentation fault", "deprecation warning"'),
-            state: z.enum(['open', 'closed', 'all']).optional().describe('Filter by issue state (default: all)'),
-            labels: z.array(z.string()).optional().describe('Filter by labels, e.g. ["bug", "help wanted"]'),
-            maxResults: z.number().optional().describe('Max results (default: 10)'),
-            sort: z.enum(['relevance', 'updated', 'created', 'comments']).optional().describe('Sort order (default: relevance). Use "updated" for most recently active issues.'),
-            package: packageSchema,
-        },
-    }, wrapTool('search_mne_issues', (args) => searchMneIssues(args, toolContext)));
-    server.registerTool('get_mne_issue', {
-        title: 'Get MNE Issue',
-        description: 'Get full details of a specific GitHub issue by number. Use after search_mne_issues to read the complete issue description and context.',
-        inputSchema: {
-            issueNumber: z.number().describe('GitHub issue number, e.g. 12345'),
-            package: packageSchema,
-        },
-    }, wrapTool('get_mne_issue', (args) => getMneIssue(args, toolContext)));
-    server.registerTool('get_mne_issue_comments', {
-        title: 'Get MNE Issue Comments',
-        description: 'Get all comments on a GitHub issue. Use to see the discussion, workarounds, and resolution for a bug or feature request.',
-        inputSchema: {
-            issueNumber: z.number().describe('GitHub issue number'),
-            package: packageSchema,
-        },
-    }, wrapTool('get_mne_issue_comments', (args) => getMneIssueComments(args, toolContext)));
-    server.registerTool('search_mne_forum', {
-        title: 'Search MNE Forum',
-        description: 'Search the MNE community Discourse forum for user questions and answers. Great for "how do I..." questions, troubleshooting, and best practices from the community.',
-        inputSchema: {
-            query: z.string().describe('Search query, e.g. "ICA artifact removal", "source localization", "EEG preprocessing"'),
-            maxResults: z.number().optional().describe('Max results (default: 5)'),
-        },
-    }, wrapTool('search_mne_forum', (args) => searchMneForum(args, toolContext)));
-    server.registerTool('get_symbol_references', {
-        title: 'Get Symbol References',
-        description: 'Find what functions a symbol calls (callees) and what calls it (callers). Use to understand code dependencies or find related functionality.',
-        inputSchema: {
-            symbol: z.string().describe('Fully qualified name, e.g. "mne.filter.filter_data"'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            crossFile: z.boolean().optional().describe('Also search for callers in other files via GitHub code search (default: false, costs extra API calls)'),
-        },
-    }, wrapTool('get_symbol_references', (args) => getSymbolReferences(args, toolContext)));
-    server.registerTool('get_mne_forum_topic', {
-        title: 'Get MNE Forum Topic',
-        description: 'Get the full content of a forum discussion including all posts. Use after search_mne_forum to read complete answers and solutions.',
-        inputSchema: {
-            topicId: z.number().describe('Forum topic ID (from search_mne_forum results URL)'),
-            maxPosts: z.number().optional().describe('Max posts to return (default: all)'),
-            maxContentLength: z.number().optional().describe('Truncate each post to N chars (default: 2000)'),
-        },
-    }, wrapTool('get_mne_forum_topic', (args) => getMneForumTopic(args, toolContext)));
-    server.registerTool('get_mne_changelog', {
-        title: 'Get MNE Changelog',
-        description: 'Get release notes for a specific MNE version. Use to find what changed between versions, new features, bug fixes, and deprecations.',
-        inputSchema: {
-            version: z.string().describe('Version number, e.g. "1.6.0"'),
-            section: z.enum(['all', 'new', 'changes', 'deprecations', 'bugfixes']).optional().describe('Filter to specific section (default: all)'),
-            package: packageSchema,
-        },
-    }, wrapTool('get_mne_changelog', (args) => getMneChangelog(args, toolContext)));
-    server.registerTool('get_mne_example', {
-        title: 'Get MNE Example',
-        description: 'Get tutorial and example code from the MNE gallery. Use when users want to see working code for a specific task like "ICA", "source localization", or "time-frequency analysis".',
-        inputSchema: {
-            query: z.string().describe('Topic to search, e.g. "epochs", "ICA", "evoked", "source estimation"'),
-            maxResults: z.number().optional().describe('Max examples to return (default: 3)'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            summaryOnly: z.boolean().optional().describe('Return only titles and descriptions, no code (default: false)'),
-            maxCodeLines: z.number().optional().describe('Truncate code to N lines (default: 100)'),
-            package: packageSchema,
-        },
-    }, wrapTool('get_mne_example', (args) => getMneExample(args, toolContext)));
-    server.registerTool('get_related_symbols', {
-        title: 'Get Related Symbols',
-        description: 'Find functions and classes related to a given symbol — same module, referenced in "See Also", or similar names. Use to discover alternative approaches or related functionality.',
-        inputSchema: {
-            symbol: z.string().describe('Fully qualified name, e.g. "mne.Epochs"'),
-            version: z.string().optional().describe('Version tag (default: latest)'),
-            maxResults: z.number().optional().describe('Max results (default: 10)'),
-        },
-    }, wrapTool('get_related_symbols', (args) => getRelatedSymbols(args, toolContext)));
-    server.registerTool('lookup_mne_error', {
-        title: 'Lookup MNE Error',
-        description: 'Diagnose MNE error messages and get solutions. Searches known issues, forum posts, and provides common fixes. Use when users paste an error traceback or ask why something failed.',
-        inputSchema: {
-            errorMessage: z.string().describe('The error message or traceback, e.g. "ValueError: No events found"'),
-            context: z.string().optional().describe('Code that caused the error (helps find better solutions)'),
-            brief: z.boolean().optional().describe('Return only descriptions, no code examples (default: false)'),
-        },
-    }, wrapTool('lookup_mne_error', (args) => lookupMneError(args, toolContext)));
+        });
+    }
     return server;
 }
 //# sourceMappingURL=server.js.map

package/dist/server.js.map

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package/dist/tools/annotations.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Default annotations for all MNE Docs MCP tools.
+ * All tools are read-only (fetch from GitHub/Discourse), non-destructive, idempotent, and call external APIs.
+ * Matches MCP ToolAnnotations (readOnlyHint, destructiveHint, idempotentHint, openWorldHint).
+ */
+export declare const READ_ONLY_TOOL_ANNOTATIONS: {
+    readonly readOnlyHint: true;
+    readonly destructiveHint: false;
+    readonly idempotentHint: true;
+    readonly openWorldHint: true;
+};
+//# sourceMappingURL=annotations.d.ts.map

package/dist/tools/annotations.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../src/tools/annotations.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,0BAA0B;;;;;CAK7B,CAAC"}

package/dist/tools/annotations.js

@@ -0,0 +1,12 @@
+/**
+ * Default annotations for all MNE Docs MCP tools.
+ * All tools are read-only (fetch from GitHub/Discourse), non-destructive, idempotent, and call external APIs.
+ * Matches MCP ToolAnnotations (readOnlyHint, destructiveHint, idempotentHint, openWorldHint).
+ */
+export const READ_ONLY_TOOL_ANNOTATIONS = {
+    readOnlyHint: true,
+    destructiveHint: false,
+    idempotentHint: true,
+    openWorldHint: true,
+};
+//# sourceMappingURL=annotations.js.map

package/dist/tools/annotations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotations.js","sourceRoot":"","sources":["../../src/tools/annotations.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,CAAC,MAAM,0BAA0B,GAAG;IACtC,YAAY,EAAE,IAAI;IAClB,eAAe,EAAE,KAAK;IACtB,cAAc,EAAE,IAAI;IACpB,aAAa,EAAE,IAAI;CACb,CAAC"}