feat(filesystem): implement MCP roots protocol for dynamic directory management

src/filesystem/README.md

@@ -9,8 +9,58 @@ Node.js server implementing Model Context Protocol (MCP) for filesystem operatio
 - Move files/directories
 - Search files
 - Get file metadata
+- Dynamic directory access control via [Roots](https://modelcontextprotocol.io/docs/concepts/roots)
+
+## Directory Access Control
+
+The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via [Roots](https://modelcontextprotocol.io/docs/concepts/roots).
+
+### Method 1: Command-line Arguments
+Specify Allowed directories when starting the server:
+```bash
+mcp-server-filesystem /path/to/dir1 /path/to/dir2
+```
+
+### Method 2: MCP Roots (Recommended)
+MCP clients that support [Roots](https://modelcontextprotocol.io/docs/concepts/roots) can dynamically update the Allowed directories. 
+
+Roots notified by Client to Server, completely replace any server-side Allowed directories when provided.
+
+**Important**: If server starts without command-line arguments AND client doesn't support roots protocol (or provides empty roots), the server will throw an error during initialization.
+
+This is the recommended method, as this enables runtime directory updates via `roots/list_changed` notifications without server restart, providing a more flexible and modern integration experience.
+
+### How It Works
+
+The server's directory access control follows this flow:
+
+1. **Server Startup**
+   - Server starts with directories from command-line arguments (if provided)
+   - If no arguments provided, server starts with empty allowed directories
+
+2. **Client Connection & Initialization**
+   - Client connects and sends `initialize` request with capabilities
+   - Server checks if client supports roots protocol (`capabilities.roots`)
+
+3. **Roots Protocol Handling** (if client supports roots)
+   - **On initialization**: Server requests roots from client via `roots/list`
+   - Client responds with its configured roots
+   - Server replaces ALL allowed directories with client's roots
+   - **On runtime updates**: Client can send `notifications/roots/list_changed`
+   - Server requests updated roots and replaces allowed directories again
+
+4. **Fallback Behavior** (if client doesn't support roots)
+   - Server continues using command-line directories only
+   - No dynamic updates possible
+
+5. **Access Control**
+   - All filesystem operations are restricted to allowed directories
+   - Use `list_allowed_directories` tool to see current directories
+   - Server requires at least ONE allowed directory to operate
+
+**Note**: The server will only allow operations within directories specified either via `args` or via Roots.
+
 
-**Note**: The server will only allow operations within directories specified via `args`.
 
 ## API
 

src/filesystem/__tests__/roots-utils.test.ts

@@ -0,0 +1,84 @@
+import { describe, it, expect, beforeEach, afterEach } from '@jest/globals';
+import { getValidRootDirectories } from '../roots-utils.js';
+import { mkdtempSync, rmSync, mkdirSync, writeFileSync, realpathSync } from 'fs';
+import { tmpdir } from 'os';
+import { join } from 'path';
+import type { Root } from '@modelcontextprotocol/sdk/types.js';
+
+describe('getValidRootDirectories', () => {
+  let testDir1: string;
+  let testDir2: string;
+  let testDir3: string;
+  let testFile: string;
+
+  beforeEach(() => {
+    // Create test directories
+    testDir1 = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-roots-test1-')));
+    testDir2 = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-roots-test2-')));
+    testDir3 = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-roots-test3-')));
+
+    // Create a test file (not a directory)
+    testFile = join(testDir1, 'test-file.txt');
+    writeFileSync(testFile, 'test content');
+  });
+
+  afterEach(() => {
+    // Cleanup
+    rmSync(testDir1, { recursive: true, force: true });
+    rmSync(testDir2, { recursive: true, force: true });
+    rmSync(testDir3, { recursive: true, force: true });
+  });
+
+  describe('valid directory processing', () => {
+    it('should process all URI formats and edge cases', async () => {
+      const roots = [
+        { uri: `file://${testDir1}`, name: 'File URI' },
+        { uri: testDir2, name: 'Plain path' },
+        { uri: testDir3 } // Plain path without name property
+      ];
+
+      const result = await getValidRootDirectories(roots);
+
+      expect(result).toContain(testDir1);
+      expect(result).toContain(testDir2);
+      expect(result).toContain(testDir3);
+      expect(result).toHaveLength(3);
+    });
+
+    it('should normalize complex paths', async () => {
+      const subDir = join(testDir1, 'subdir');
+      mkdirSync(subDir);
+
+      const roots = [
+        { uri: `file://${testDir1}/./subdir/../subdir`, name: 'Complex Path' }
+      ];
+
+      const result = await getValidRootDirectories(roots);
+
+      expect(result).toHaveLength(1);
+      expect(result[0]).toBe(subDir);
+    });
+  });
+
+  describe('error handling', () => {
+
+    it('should handle various error types', async () => {
+      const nonExistentDir = join(tmpdir(), 'non-existent-directory-12345');
+      const invalidPath = '\0invalid\0path'; // Null bytes cause different error types
+      const roots = [
+        { uri: `file://${testDir1}`, name: 'Valid Dir' },
+        { uri: `file://${nonExistentDir}`, name: 'Non-existent Dir' },
+        { uri: `file://${testFile}`, name: 'File Not Dir' },
+        { uri: `file://${invalidPath}`, name: 'Invalid Path' }
+      ];
+
+      const result = await getValidRootDirectories(roots);
+
+      expect(result).toContain(testDir1);
+      expect(result).not.toContain(nonExistentDir);
+      expect(result).not.toContain(testFile);
+      expect(result).not.toContain(invalidPath);
+      expect(result).toHaveLength(1);
+    });
+  });
+});

src/filesystem/index.ts

@@ -6,6 +6,8 @@ import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
   ToolSchema,
+  RootsListChangedNotificationSchema,
+  type Root,
 } from "@modelcontextprotocol/sdk/types.js";
 import fs from "fs/promises";
 import path from "path";
@@ -16,12 +18,16 @@ import { zodToJsonSchema } from "zod-to-json-schema";
 import { diffLines, createTwoFilesPatch } from 'diff';
 import { minimatch } from 'minimatch';
 import { isPathWithinAllowedDirectories } from './path-validation.js';
+import { getValidRootDirectories } from './roots-utils.js';
 
 // Command line argument parsing
 const args = process.argv.slice(2);
 if (args.length === 0) {
-  console.error("Usage: mcp-server-filesystem <allowed-directory> [additional-directories...]");
-  process.exit(1);
+  console.error("Usage: mcp-server-filesystem [allowed-directory] [additional-directories...]");
+  console.error("Note: Allowed directories can be provided via:");
+  console.error("  1. Command-line arguments (shown above)");
+  console.error("  2. MCP roots protocol (if client supports it)");
+  console.error("At least one directory must be provided by EITHER method for the server to operate.");
 }
 
 // Normalize all paths consistently
@@ -37,7 +43,7 @@ function expandHome(filepath: string): string {
 }
 
 // Store allowed directories in normalized and resolved form
-const allowedDirectories = await Promise.all(
+let allowedDirectories = await Promise.all(
   args.map(async (dir) => {
     const expanded = expandHome(dir);
     const absolute = path.resolve(expanded);
@@ -573,8 +579,8 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
       {
         name: "list_allowed_directories",
         description:
-          "Returns the list of directories that this server is allowed to access. " +
-          "Use this to understand which directories are available before trying to access files.",
+          "Returns the list of root directories that this server is allowed to access. " +
+          "Use this to understand which directories are available before trying to access files. ",
         inputSchema: {
           type: "object",
           properties: {},
@@ -890,12 +896,62 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
   }
 });
 
+// Updates allowed directories based on MCP client roots
+async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
+  const validatedRootDirs = await getValidRootDirectories(requestedRoots);
+  if (validatedRootDirs.length > 0) {
+    allowedDirectories = [...validatedRootDirs];
+    console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
+  } else {
+    console.error("No valid root directories provided by client");
+  }
+}
+
+// Handles dynamic roots updates during runtime, when client sends "roots/list_changed" notification, server fetches the updated roots and replaces all allowed directories with the new roots.
+server.setNotificationHandler(RootsListChangedNotificationSchema, async () => {
+  try {
+    // Request the updated roots list from the client
+    const response = await server.listRoots();
+    if (response && 'roots' in response) {
+      await updateAllowedDirectoriesFromRoots(response.roots);
+    }
+  } catch (error) {
+    console.error("Failed to request roots from client:", error instanceof Error ? error.message : String(error));
+  }
+});
+
+// Handles post-initialization setup, specifically checking for and fetching MCP roots.
+server.oninitialized = async () => {
+  const clientCapabilities = server.getClientCapabilities();
+
+  if (clientCapabilities?.roots) {
+    try {
+      const response = await server.listRoots();
+      if (response && 'roots' in response) {
+        await updateAllowedDirectoriesFromRoots(response.roots);
+      } else {
+        console.error("Client returned no roots set, keeping current settings");
+      }
+    } catch (error) {
+      console.error("Failed to request initial roots from client:", error instanceof Error ? error.message : String(error));
+    }
+  } else {
+    if (allowedDirectories.length > 0) {
+      console.error("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
+    }else{
+      throw new Error(`Server cannot operate: No allowed directories available. Server was started without command-line directories and client either does not support MCP roots protocol or provided empty roots. Please either: 1) Start server with directory arguments, or 2) Use a client that supports MCP roots protocol and provides valid root directories.`);
+    }
+  }
+};
+
 // Start server
 async function runServer() {
   const transport = new StdioServerTransport();
   await server.connect(transport);
   console.error("Secure MCP Filesystem Server running on stdio");
-  console.error("Allowed directories:", allowedDirectories);
+  if (allowedDirectories.length === 0) {
+    console.error("Started without allowed directories - waiting for client to provide roots via MCP protocol");
+  }
 }
 
 runServer().catch((error) => {

src/filesystem/roots-utils.ts

@@ -0,0 +1,76 @@
+import { promises as fs, type Stats } from 'fs';
+import path from 'path';
+import os from 'os';
+import { normalizePath } from './path-utils.js';
+import type { Root } from '@modelcontextprotocol/sdk/types.js';
+
+/**
+ * Converts a root URI to a normalized directory path with basic security validation.
+ * @param rootUri - File URI (file://...) or plain directory path
+ * @returns Promise resolving to validated path or null if invalid
+ */
+async function parseRootUri(rootUri: string): Promise<string | null> {
+  try {
+    const rawPath = rootUri.startsWith('file://') ? rootUri.slice(7) : rootUri;
+    const expandedPath = rawPath.startsWith('~/') || rawPath === '~' 
+      ? path.join(os.homedir(), rawPath.slice(1)) 
+      : rawPath;
+    const absolutePath = path.resolve(expandedPath);
+    const resolvedPath = await fs.realpath(absolutePath);
+    return normalizePath(resolvedPath);
+  } catch {
+    return null; // Path doesn't exist or other error
+  }
+}
+
+/**
+ * Formats error message for directory validation failures.
+ * @param dir - Directory path that failed validation
+ * @param error - Error that occurred during validation
+ * @param reason - Specific reason for failure
+ * @returns Formatted error message
+ */
+function formatDirectoryError(dir: string, error?: unknown, reason?: string): string {
+  if (reason) {
+    return `Skipping ${reason}: ${dir}`;
+  }
+  const message = error instanceof Error ? error.message : String(error);
+  return `Skipping invalid directory: ${dir} due to error: ${message}`;
+}
+
+/**
+ * Resolves requested root directories from MCP root specifications.
+ * 
+ * Converts root URI specifications (file:// URIs or plain paths) into normalized
+ * directory paths, validating that each path exists and is a directory.
+ * Includes symlink resolution for security.
+ * 
+ * @param requestedRoots - Array of root specifications with URI and optional name
+ * @returns Promise resolving to array of validated directory paths
+ */
+export async function getValidRootDirectories(
+  requestedRoots: readonly Root[]
+): Promise<string[]> {
+  const validatedDirectories: string[] = [];
+
+  for (const requestedRoot of requestedRoots) {
+    const resolvedPath = await parseRootUri(requestedRoot.uri);
+    if (!resolvedPath) {
+      console.error(formatDirectoryError(requestedRoot.uri, undefined, 'invalid path or inaccessible'));
+      continue;
+    }
+
+    try {
+      const stats: Stats = await fs.stat(resolvedPath);
+      if (stats.isDirectory()) {
+        validatedDirectories.push(resolvedPath);
+      } else {
+        console.error(formatDirectoryError(resolvedPath, undefined, 'non-directory root'));
+      }
+    } catch (error) {
+      console.error(formatDirectoryError(resolvedPath, error));
+    }
+  }
+
+  return validatedDirectories;
+}