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/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;
+}