diff --git a/src/resource-loader.ts b/src/resource-loader.ts
index ad60e1c03..deb6e1d87 100644
--- a/src/resource-loader.ts
+++ b/src/resource-loader.ts
@@ -87,9 +87,13 @@ function writeManagedResourceManifest(agentDir: string): void {
       installedExtensionDirs = entries
         .filter(e => e.isDirectory())
         .filter(e => {
-          // Only track directories that are actual extensions (contain index.js or index.ts)
+          // Track directories that are actual extensions — identified by an
+          // index.js/index.ts entry point OR an extension-manifest.json (e.g.
+          // remote-questions which uses mod.ts instead of index.ts).
           const dirPath = join(bundledExtensionsDir, e.name)
-          return existsSync(join(dirPath, 'index.js')) || existsSync(join(dirPath, 'index.ts'))
+          return existsSync(join(dirPath, 'index.js'))
+            || existsSync(join(dirPath, 'index.ts'))
+            || existsSync(join(dirPath, 'extension-manifest.json'))
         })
         .map(e => e.name)
     }
diff --git a/src/tests/resource-loader.test.ts b/src/tests/resource-loader.test.ts
index 12622a1ad..637b9088a 100644
--- a/src/tests/resource-loader.test.ts
+++ b/src/tests/resource-loader.test.ts
@@ -1,6 +1,6 @@
 import test from "node:test";
 import assert from "node:assert/strict";
-import { existsSync, mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { existsSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
 import { join, parse } from "node:path";
 import { tmpdir } from "node:os";
 
@@ -98,6 +98,39 @@ test("buildResourceLoader excludes duplicate top-level pi extensions when bundle
   );
 });
 
+test("initResources manifest tracks all bundled extension subdirectories including remote-questions (#2367)", async () => {
+  const { initResources } = await import("../resource-loader.ts");
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-resource-loader-manifest-"));
+  const fakeAgentDir = join(tmp, "agent");
+
+  try {
+    initResources(fakeAgentDir);
+
+    const manifestPath = join(fakeAgentDir, "managed-resources.json");
+    assert.equal(existsSync(manifestPath), true, "managed-resources.json should exist after initResources");
+
+    const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
+    const installedDirs: string[] = manifest.installedExtensionDirs ?? [];
+
+    // remote-questions uses mod.ts (not index.ts) as its entry point and has an
+    // extension-manifest.json — it must still appear in the manifest so that
+    // pruneRemovedBundledExtensions can track it across upgrades.
+    assert.ok(
+      installedDirs.includes("remote-questions"),
+      `installedExtensionDirs should include remote-questions but got: [${installedDirs.join(", ")}]`,
+    );
+
+    // Also verify that the synced remote-questions directory actually exists in the agent dir
+    assert.equal(
+      existsSync(join(fakeAgentDir, "extensions", "remote-questions")),
+      true,
+      "remote-questions directory should be synced to agent extensions",
+    );
+  } finally {
+    rmSync(tmp, { recursive: true, force: true });
+  }
+});
+
 test("initResources prunes stale top-level extension siblings next to bundled compiled extensions", async (t) => {
   const { initResources } = await import("../resource-loader.ts");
   const tmp = mkdtempSync(join(tmpdir(), "gsd-resource-loader-sync-"));