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

- Extract roots processing logic from index.ts into testable roots-utils.ts module and add Test suite
- Update README to recommend MCP roots protocol for dynamic directory management

src/filesystem/README.md

@@ -16,13 +16,19 @@ Node.js server implementing Model Context Protocol (MCP) for filesystem operatio
 The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via the MCP roots protocol.
 
 ### Method 1: Command-line Arguments
-Specify allowed directories when starting the server:
+Specify Allowed directories when starting the server:
 ```bash
 mcp-server-filesystem /path/to/dir1 /path/to/dir2
 ```
 
-### Method 2: MCP Roots Protocol  
-MCP clients that support the roots protocol can dynamically provide allowed directories. Client roots completely replace any command-line directories when provided.
+### Method 2: MCP Roots Protocol (Recommended)
+MCP clients that support the roots protocol 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 MCP roots protocol for dynamic directory management. This enables runtime directory updates via `roots/list_changed` notifications without server restart, providing a more flexible and modern integration experience.
 
 ### How It Works
 
@@ -52,7 +58,9 @@ The server's directory access control follows this flow:
    - Use `list_allowed_directories` tool to see current directories
    - Server requires at least ONE allowed directory to operate
 
-**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.
+**Note**: The server will only allow operations within directories specified either via `args` or via Roots.
+
+
 
 ## 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

@@ -7,6 +7,7 @@ import {
   ListToolsRequestSchema,
   ToolSchema,
   RootsListChangedNotificationSchema,
+  type Root,
 } from "@modelcontextprotocol/sdk/types.js";
 import fs from "fs/promises";
 import path from "path";
@@ -17,6 +18,7 @@ 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);
@@ -894,26 +896,10 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
   }
 });
 
-// Replaces any existing allowed directories based on roots provided by the MCP client.
-async function updateAllowedDirectoriesFromRoots(roots: Array<{ uri: string; name?: string }>) {
-  const rootDirs: string[] = [];
-  for (const root of roots) {
-    let dir: string;
-    // Handle both file:// URIs (MCP standard) and plain directory paths (for flexibility)
-    dir = normalizePath(path.resolve(root.uri.startsWith('file://')? root.uri.slice(7) : root.uri));
-    try {
-      const stats = await fs.stat(dir);
-      if (stats.isDirectory()) {
-        rootDirs.push(dir);
-      }else {
-        console.error(`Skipping non-directory root: ${dir}`);
-      }
-    } catch (error) {
-      // Skip invalid directories
-      console.error(`Skipping invalid directory: ${dir} due to error:`, error instanceof Error ? error.message : String(error));
-    }
-  }
-  if(rootDirs.length > 0) {
+// Updates allowed directories based on MCP client roots
+async function updateAllowedDirectoriesFromRoots(roots: Root[]) {
+  const rootDirs = await getValidRootDirectories(roots);
+  if (rootDirs.length > 0) {
     allowedDirectories.splice(0, allowedDirectories.length, ...rootDirs);
   }
 }
@@ -941,16 +927,16 @@ server.oninitialized = async () => {
       if (response && 'roots' in response) {
         await updateAllowedDirectoriesFromRoots(response.roots);
       } else {
-        console.error("Client returned no roots set, keeping current settings");
+        console.log("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);
+      console.log("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 does not support MCP roots protocol. Please either: 1) Start server with directory arguments, or 2) Use a client that supports MCP roots protocol.`);
+      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.`);
     }
   }
 };
@@ -961,7 +947,7 @@ async function runServer() {
   await server.connect(transport);
   console.error("Secure MCP Filesystem Server running on stdio");
   if (allowedDirectories.length === 0) {
-    console.error("Started without allowed directories - waiting for client to provide roots via MCP protocol");
+    console.log("Started without allowed directories - waiting for client to provide roots via MCP protocol");
   }
 }
 

src/filesystem/roots-utils.ts

@@ -0,0 +1,61 @@
+import { promises as fs, type Stats } from 'fs';
+import path from 'path';
+import { normalizePath } from './path-utils.js';
+import type { Root } from '@modelcontextprotocol/sdk/types.js';
+
+/**
+ * Converts a root URI to a normalized directory path.
+ * @param uri - File URI (file://...) or plain directory path
+ * @returns Normalized absolute directory path
+ */
+function parseRootUri(uri: string): string {
+  const rawPath = uri.startsWith('file://') ? uri.slice(7) : uri;
+  return normalizePath(path.resolve(rawPath));
+}
+
+/**
+ * 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}`;
+}
+
+/**
+ * Gets valid directory paths 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.
+ * 
+ * @param roots - Array of root specifications with URI and optional name
+ * @returns Promise resolving to array of validated directory paths
+ */
+export async function getValidRootDirectories(
+  roots: readonly Root[]
+): Promise<string[]> {
+  const validDirectories: string[] = [];
+  
+  for (const root of roots) {
+    const dir = parseRootUri(root.uri);
+    
+    try {
+      const stats: Stats = await fs.stat(dir);
+      if (stats.isDirectory()) {
+        validDirectories.push(dir);
+      } else {
+        console.error(formatDirectoryError(dir, undefined, 'non-directory root'));
+      }
+    } catch (error) {
+      console.error(formatDirectoryError(dir, error));
+    }
+  }
+  
+  return validDirectories;
+}