diff --git a/apps/desktop/main/protocol.ts b/apps/desktop/main/protocol.ts
index 460b153a..cc3c75b9 100644
--- a/apps/desktop/main/protocol.ts
+++ b/apps/desktop/main/protocol.ts
@@ -59,6 +59,8 @@ let activeThemeId = 'peek';
 
 // Root directory (set during init)
 let rootDir: string;
+// node_modules lives at the repo root (two levels above apps/desktop)
+let nodeModulesDir: string;
 
 // Bare import map for resolving npm package imports
 // Maps bare specifiers (e.g., 'lit') to node_modules paths
@@ -287,7 +289,7 @@ async function handleProtocolRequest(req: Request): Promise<Response> {
 
     if (resolvedPath) {
       DEBUG && console.log(`[protocol] Resolved bare import: ${bareSpecifier} -> ${resolvedPath}`);
-      const absolutePath = path.resolve(rootDir, resolvedPath);
+      const absolutePath = path.resolve(nodeModulesDir, resolvedPath);
       return fetchFile(absolutePath, req.url);
     }
 
@@ -675,7 +677,9 @@ async function handleProtocolRequest(req: Request): Promise<Response> {
       relativePath = path.join(host, pathname);
     }
 
-    const absolutePath = path.resolve(rootDir, relativePath);
+    // node_modules are at the repo root, not under apps/desktop
+    const resolveBase = (host === 'node_modules') ? nodeModulesDir : rootDir;
+    const absolutePath = path.resolve(resolveBase, relativePath);
 
     return fetchFile(absolutePath, req.url);
   } catch (err) {
@@ -701,6 +705,8 @@ async function handleProtocolRequest(req: Request): Promise<Response> {
  */
 export function initProtocol(appRootDir: string): void {
   rootDir = appRootDir;
+  // node_modules is at the repo root (../../ from apps/desktop)
+  nodeModulesDir = path.join(rootDir, '../..');
   protocol.handle(APP_SCHEME, handleProtocolRequest);
 }
 
diff --git a/apps/desktop/tests/components/components.spec.ts b/apps/desktop/tests/components/components.spec.ts
index 8608efc4..82de72f0 100644
--- a/apps/desktop/tests/components/components.spec.ts
+++ b/apps/desktop/tests/components/components.spec.ts
@@ -15,7 +15,7 @@ import { readFileSync, existsSync } from 'fs';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const ROOT = path.join(__dirname, '../..');
+const ROOT = path.join(__dirname, '../../../..');
 
 // Simple static file server
 let server: ReturnType<typeof createServer>;
@@ -39,7 +39,7 @@ function startServer(): Promise<string> {
       }
 
       // Handle component imports
-      if (req.url?.startsWith('/app/components/')) {
+      if (req.url?.startsWith('/apps/desktop/renderer/') || req.url?.startsWith('/app/components/')) {
         filePath = path.join(ROOT, req.url);
       }
 
diff --git a/apps/desktop/tests/components/test-page.html b/apps/desktop/tests/components/test-page.html
index 6c7ef5c3..0a76d937 100644
--- a/apps/desktop/tests/components/test-page.html
+++ b/apps/desktop/tests/components/test-page.html
@@ -290,7 +290,7 @@
 
   <script type="module">
     // Import all components
-    import '/app/components/index.js';
+    import '/apps/desktop/renderer/components/index.js';
 
     // Setup test helpers
     window.testHelpers = {
diff --git a/apps/desktop/tests/desktop/lists-tile.spec.ts b/apps/desktop/tests/desktop/lists-tile.spec.ts
index 70504c77..ff11aec0 100644
--- a/apps/desktop/tests/desktop/lists-tile.spec.ts
+++ b/apps/desktop/tests/desktop/lists-tile.spec.ts
@@ -36,7 +36,7 @@ test.describe('Lists Tile @desktop', () => {
     // command invocation; keepLive preserves it once spawned.
     const fs = await import('node:fs');
     const path = await import('node:path');
-    const manifestPath = path.resolve(process.cwd(), 'features/lists/manifest.json');
+    const manifestPath = path.resolve(process.cwd(), 'apps/desktop/features/lists/manifest.json');
     const manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf8'));
     expect(manifest.tiles).toHaveLength(1);
     expect(manifest.tiles[0].id).toBe('home');
diff --git a/apps/desktop/tests/editor/editor-folding.spec.ts b/apps/desktop/tests/editor/editor-folding.spec.ts
index f4dd6d24..86995966 100644
--- a/apps/desktop/tests/editor/editor-folding.spec.ts
+++ b/apps/desktop/tests/editor/editor-folding.spec.ts
@@ -16,7 +16,7 @@ import { readFileSync, existsSync } from 'fs';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const ROOT = path.join(__dirname, '../..');
+const ROOT = path.join(__dirname, '../../../..');
 
 // Simple static file server
 let server: ReturnType<typeof createServer>;
diff --git a/apps/desktop/tests/editor/editor-layout.spec.ts b/apps/desktop/tests/editor/editor-layout.spec.ts
index f86abddf..0d1bdf46 100644
--- a/apps/desktop/tests/editor/editor-layout.spec.ts
+++ b/apps/desktop/tests/editor/editor-layout.spec.ts
@@ -17,7 +17,7 @@ import { readFileSync, existsSync } from 'fs';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const ROOT = path.join(__dirname, '../..');
+const ROOT = path.join(__dirname, '../../../..');
 
 // Simple static file server
 let server: ReturnType<typeof createServer>;
diff --git a/apps/desktop/tests/editor/test-layout-page.html b/apps/desktop/tests/editor/test-layout-page.html
index 98712b66..697b84c6 100644
--- a/apps/desktop/tests/editor/test-layout-page.html
+++ b/apps/desktop/tests/editor/test-layout-page.html
@@ -231,7 +231,7 @@
   <div id="editor-root"></div>
 
   <script type="module">
-    import { EditorLayout } from '/features/editor/editor-layout.js';
+    import { EditorLayout } from '/apps/desktop/features/editor/editor-layout.js';
 
     const TEST_CONTENT = `# Introduction
 
diff --git a/apps/desktop/tests/fixtures/extension-app.ts b/apps/desktop/tests/fixtures/extension-app.ts
index d267f16c..3938de0e 100644
--- a/apps/desktop/tests/fixtures/extension-app.ts
+++ b/apps/desktop/tests/fixtures/extension-app.ts
@@ -28,7 +28,7 @@ import { sleep } from '../helpers/window-utils';
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
 const ROOT = path.join(__dirname, '../..');
-const EXTENSION_PATH = path.join(ROOT, 'backend/extension');
+const EXTENSION_PATH = path.join(__dirname, '../../../../backend/extension');
 
 export type ExtensionBrowser = 'chrome' | 'firefox';