diff --git a/src/filesystem/__tests__/path-utils.test.ts b/src/filesystem/__tests__/path-utils.test.ts
index 5530cba1c3..a4d4a0cc4b 100644
--- a/src/filesystem/__tests__/path-utils.test.ts
+++ b/src/filesystem/__tests__/path-utils.test.ts
@@ -195,7 +195,7 @@ describe('Path Utilities', () => {
       // UNC paths should preserve the leading double backslash
       const uncPath = '\\\\SERVER\\share\\folder';
       expect(normalizePath(uncPath)).toBe('\\\\SERVER\\share\\folder');
-      
+
       // Test UNC path with double backslashes that need normalization
       const uncPathWithDoubles = '\\\\\\\\SERVER\\\\share\\\\folder';
       expect(normalizePath(uncPathWithDoubles)).toBe('\\\\SERVER\\share\\folder');
@@ -222,6 +222,19 @@ describe('Path Utilities', () => {
       expect(result.length).toBeGreaterThan(0);
     });
 
+    it('leaves literal ~MyFolder unchanged (not home expansion)', () => {
+      expect(expandHome('~MyFolder')).toBe('~MyFolder');
+    });
+
+    it('leaves ~user unchanged (not home expansion)', () => {
+      expect(expandHome('~user')).toBe('~user');
+    });
+
+    it('leaves paths with tilde in the middle unchanged', () => {
+      expect(expandHome('/Volumes/Drive/Projects/~MyFolder')).toBe('/Volumes/Drive/Projects/~MyFolder');
+      expect(expandHome('/home/user/~backup')).toBe('/home/user/~backup');
+    });
+
     it('leaves other paths unchanged', () => {
       expect(expandHome('C:/test')).toBe('C:/test');
     });
diff --git a/src/filesystem/__tests__/path-validation.test.ts b/src/filesystem/__tests__/path-validation.test.ts
index 81ad247ee2..32c01a4ac4 100644
--- a/src/filesystem/__tests__/path-validation.test.ts
+++ b/src/filesystem/__tests__/path-validation.test.ts
@@ -12,10 +12,10 @@ async function checkSymlinkSupport(): Promise<boolean> {
   try {
     const targetFile = path.join(testDir, 'target.txt');
     const linkFile = path.join(testDir, 'link.txt');
-    
+
     await fs.writeFile(targetFile, 'test');
     await fs.symlink(targetFile, linkFile);
-    
+
     // If we get here, symlinks are supported
     return true;
   } catch (error) {
@@ -240,7 +240,11 @@ describe('Path Validation', () => {
 
       // But only on the same filesystem root
       if (path.sep === '\\') {
-        expect(isPathWithinAllowedDirectories('D:\\other', ['/'])).toBe(false);
+        // '/' resolves to the current drive root on Windows, so we must
+        // test with a drive letter that differs from the CWD's drive.
+        const cwdDrive = process.cwd().charAt(0).toUpperCase();
+        const otherDrive = cwdDrive === 'D' ? 'C' : 'D';
+        expect(isPathWithinAllowedDirectories(`${otherDrive}:\\other`, ['/'])).toBe(false);
       }
     });
   });
diff --git a/src/filesystem/__tests__/roots-utils.test.ts b/src/filesystem/__tests__/roots-utils.test.ts
index 1a39483953..1c930e797e 100644
--- a/src/filesystem/__tests__/roots-utils.test.ts
+++ b/src/filesystem/__tests__/roots-utils.test.ts
@@ -48,7 +48,7 @@ describe('getValidRootDirectories', () => {
     it('should normalize complex paths', async () => {
       const subDir = join(testDir1, 'subdir');
       mkdirSync(subDir);
-      
+
       const roots = [
         { uri: `file://${testDir1}/./subdir/../subdir`, name: 'Complex Path' }
       ];
@@ -81,4 +81,36 @@ describe('getValidRootDirectories', () => {
       expect(result).toHaveLength(1);
     });
   });
+
+  describe('tilde-prefixed directory names', () => {
+    let tildeDir: string;
+
+    beforeEach(() => {
+      // Create a directory with a tilde-prefixed name inside testDir1
+      tildeDir = join(testDir1, '~MyFolder');
+      mkdirSync(tildeDir);
+    });
+
+    it('should handle directory names starting with tilde as literal names', async () => {
+      const roots = [
+        { uri: tildeDir, name: 'Tilde Dir' }
+      ];
+
+      const result = await getValidRootDirectories(roots);
+
+      expect(result).toHaveLength(1);
+      expect(result[0]).toContain('~MyFolder');
+    });
+
+    it('should handle file:// URIs with tilde-prefixed directory names', async () => {
+      const roots = [
+        { uri: `file://${tildeDir}`, name: 'Tilde Dir URI' }
+      ];
+
+      const result = await getValidRootDirectories(roots);
+
+      expect(result).toHaveLength(1);
+      expect(result[0]).toContain('~MyFolder');
+    });
+  });
 });
\ No newline at end of file
diff --git a/src/filesystem/__tests__/startup-validation.test.ts b/src/filesystem/__tests__/startup-validation.test.ts
index 3be283df74..26c3821cf1 100644
--- a/src/filesystem/__tests__/startup-validation.test.ts
+++ b/src/filesystem/__tests__/startup-validation.test.ts
@@ -97,4 +97,15 @@ describe('Startup Directory Validation', () => {
     // Should still start with the valid directory
     expect(result.stderr).toContain('Secure MCP Filesystem Server running on stdio');
   });
+
+  it('should start successfully with tilde-prefixed directory name', async () => {
+    const tildeDir = path.join(testDir, '~MyFolder');
+    await fs.mkdir(tildeDir, { recursive: true });
+
+    const result = await spawnServer([tildeDir]);
+
+    // Server should start without errors
+    expect(result.stderr).toContain('Secure MCP Filesystem Server running on stdio');
+    expect(result.stderr).not.toContain('Error:');
+  });
 });
diff --git a/src/filesystem/index.ts b/src/filesystem/index.ts
index a515df7c61..acaa3f48e6 100644
--- a/src/filesystem/index.ts
+++ b/src/filesystem/index.ts
@@ -499,8 +499,7 @@ server.registerTool(
 
     // Format the output
     const formattedEntries = sortedEntries.map(entry =>
-      `${entry.isDirectory ? "[DIR]" : "[FILE]"} ${entry.name.padEnd(30)} ${
-        entry.isDirectory ? "" : formatSize(entry.size).padStart(10)
+      `${entry.isDirectory ? "[DIR]" : "[FILE]"} ${entry.name.padEnd(30)} ${entry.isDirectory ? "" : formatSize(entry.size).padStart(10)
       }`
     );
 
@@ -710,7 +709,8 @@ async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
     setAllowedDirectories(allowedDirectories); // Update the global state in lib.ts
     console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
   } else {
-    console.error("No valid root directories provided by client");
+    console.error("Error: No valid root directories provided by client. Received roots:",
+      JSON.stringify(requestedRoots.map(r => r.uri)));
   }
 }
 
@@ -745,7 +745,7 @@ server.server.oninitialized = async () => {
   } else {
     if (allowedDirectories.length > 0) {
       console.error("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
-    }else{
+    } 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.`);
     }
   }
diff --git a/src/filesystem/path-utils.ts b/src/filesystem/path-utils.ts
index 50910b995b..9d21315dd4 100644
--- a/src/filesystem/path-utils.ts
+++ b/src/filesystem/path-utils.ts
@@ -106,7 +106,9 @@ export function normalizePath(p: string): string {
 }
 
 /**
- * Expands home directory tildes in paths
+ * Expands home directory tildes in paths.
+ * Only expands `~` (bare) or `~/...` (home-prefixed) paths.
+ * Literal folder names like `~MyFolder` are intentionally left unchanged.
  * @param filepath The path to expand
  * @returns Expanded path
  */
diff --git a/src/filesystem/roots-utils.ts b/src/filesystem/roots-utils.ts
index 5e26bb246b..445bc8a5e6 100644
--- a/src/filesystem/roots-utils.ts
+++ b/src/filesystem/roots-utils.ts
@@ -1,7 +1,6 @@
 import { promises as fs, type Stats } from 'fs';
 import path from 'path';
-import os from 'os';
-import { normalizePath } from './path-utils.js';
+import { normalizePath, expandHome } from './path-utils.js';
 import type { Root } from '@modelcontextprotocol/sdk/types.js';
 import { fileURLToPath } from "url";
 
@@ -13,14 +12,14 @@ import { fileURLToPath } from "url";
 async function parseRootUri(rootUri: string): Promise<string | null> {
   try {
     const rawPath = rootUri.startsWith('file://') ? fileURLToPath(rootUri) : rootUri;
-    const expandedPath = rawPath.startsWith('~/') || rawPath === '~' 
-      ? path.join(os.homedir(), rawPath.slice(1)) 
-      : rawPath;
+    const expandedPath = expandHome(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
+  } catch (error) {
+    const message = error instanceof Error ? error.message : String(error);
+    console.error(`Failed to resolve root URI "${rootUri}": ${message}`);
+    return null;
   }
 }
 
@@ -53,14 +52,14 @@ 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()) {
@@ -72,6 +71,6 @@ export async function getValidRootDirectories(
       console.error(formatDirectoryError(resolvedPath, error));
     }
   }
-  
+
   return validatedDirectories;
 }
\ No newline at end of file