fix(filesystem): preserve CLI directories when merging with MCP roots

The oninitialized and roots/list_changed handlers replaced all
CLI-provided allowed directories with client roots, silently
discarding any extra directories passed via command-line arguments.

Store CLI directories as an immutable baseline and merge them with
client roots using a Set for deduplication. When roots become empty
or invalid, fall back to the CLI baseline instead of keeping stale
roots.

Fixes #3602

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Bingtagui404

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

@@ -1,5 +1,5 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { getValidRootDirectories } from '../roots-utils.js';
+import { getValidRootDirectories, mergeAllowedDirectories } from '../roots-utils.js';
 import { mkdtempSync, rmSync, mkdirSync, writeFileSync, realpathSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
@@ -81,4 +81,33 @@ describe('getValidRootDirectories', () => {
       expect(result).toHaveLength(1);
     });
   });
-});
+});
+
+describe('mergeAllowedDirectories', () => {
+  it('preserves CLI directories while adding current client roots', () => {
+    const result = mergeAllowedDirectories(
+      ['/cli/one', '/cli/two'],
+      ['/roots/current']
+    );
+
+    expect(result).toEqual(['/cli/one', '/cli/two', '/roots/current']);
+  });
+
+  it('deduplicates directories shared by CLI args and client roots', () => {
+    const result = mergeAllowedDirectories(
+      ['/shared', '/cli/only'],
+      ['/shared', '/roots/only']
+    );
+
+    expect(result).toEqual(['/shared', '/cli/only', '/roots/only']);
+  });
+
+  it('falls back to the CLI baseline when the client provides no valid roots', () => {
+    const result = mergeAllowedDirectories(
+      ['/cli/one', '/cli/two'],
+      []
+    );
+
+    expect(result).toEqual(['/cli/one', '/cli/two']);
+  });
+});

src/filesystem/index.ts

@@ -13,7 +13,7 @@ import path from "path";
 import { z } from "zod";
 import { minimatch } from "minimatch";
 import { normalizePath, expandHome } from './path-utils.js';
-import { getValidRootDirectories } from './roots-utils.js';
+import { getValidRootDirectories, mergeAllowedDirectories } from './roots-utils.js';
 import {
   // Function imports
   formatSize,
@@ -89,6 +89,11 @@ if (accessibleDirectories.length === 0 && allowedDirectories.length > 0) {
 
 allowedDirectories = accessibleDirectories;
 
+// Preserve CLI-provided directories for merging with MCP roots later.
+// CLI directories are explicitly set by the administrator and must not be
+// discarded when the client provides roots via the MCP roots protocol.
+const cliAllowedDirectories = [...allowedDirectories];
+
 // Initialize the global allowedDirectories in lib.ts
 setAllowedDirectories(allowedDirectories);
 
@@ -702,15 +707,17 @@ server.registerTool(
   }
 );
 
-// Updates allowed directories based on MCP client roots
+// Updates allowed directories by merging CLI-provided directories with MCP client roots.
+// CLI directories are always preserved; client roots are added on top of them.
 async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
   const validatedRootDirs = await getValidRootDirectories(requestedRoots);
+  allowedDirectories = mergeAllowedDirectories(cliAllowedDirectories, validatedRootDirs);
+  setAllowedDirectories(allowedDirectories);
+
   if (validatedRootDirs.length > 0) {
-    allowedDirectories = [...validatedRootDirs];
-    setAllowedDirectories(allowedDirectories); // Update the global state in lib.ts
-    console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
+    console.error(`Allowed directories: ${cliAllowedDirectories.length} from CLI + ${validatedRootDirs.length} from MCP roots (${allowedDirectories.length} total after dedup)`);
   } else {
-    console.error("No valid root directories provided by client");
+    console.error(`No valid root directories provided by client, using ${cliAllowedDirectories.length} CLI directory${cliAllowedDirectories.length === 1 ? '' : 'ies'}`);
   }
 }
 

src/filesystem/roots-utils.ts

@@ -74,4 +74,17 @@ export async function getValidRootDirectories(
   }
 
   return validatedDirectories;
-}
+}
+
+/**
+ * Merges the fixed CLI directory baseline with the current client-provided roots.
+ *
+ * The merge is recalculated from scratch each time so outdated roots do not linger
+ * after a roots/list_changed update.
+ */
+export function mergeAllowedDirectories(
+  cliAllowedDirectories: readonly string[],
+  rootDirectories: readonly string[]
+): string[] {
+  return [...new Set([...cliAllowedDirectories, ...rootDirectories])];
+}