diff --git a/src/cli.ts b/src/cli.ts
index d4f59cb44..ac25bb18c 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -470,8 +470,8 @@ if (isPrintMode) {
   if (extensionsResult.errors.length > 0) {
     for (const err of extensionsResult.errors) {
       // Downgrade conflicts with built-in tools to warnings (#1347)
-      const isSuperseded = err.error.includes("supersedes");
-      const prefix = isSuperseded ? "Extension conflict" : "Extension load error";
+      const isConflict = err.error.includes("supersedes") || err.error.includes("conflicts with");
+      const prefix = isConflict ? "Extension conflict" : "Extension load error";
       process.stderr.write(`[gsd] ${prefix}: ${err.error}\n`)
     }
   }
@@ -622,8 +622,8 @@ validateConfiguredModel(modelRegistry, settingsManager)
 
 if (extensionsResult.errors.length > 0) {
   for (const err of extensionsResult.errors) {
-    const isSuperseded = err.error.includes("supersedes");
-    const prefix = isSuperseded ? "Extension conflict" : "Extension load error";
+    const isConflict = err.error.includes("supersedes") || err.error.includes("conflicts with");
+    const prefix = isConflict ? "Extension conflict" : "Extension load error";
     process.stderr.write(`[gsd] ${prefix}: ${err.error}\n`)
   }
 }
diff --git a/src/resource-loader.ts b/src/resource-loader.ts
index 041d53143..30ad9c21d 100644
--- a/src/resource-loader.ts
+++ b/src/resource-loader.ts
@@ -373,6 +373,16 @@ function pruneRemovedBundledExtensions(
     }
   }
 
+  // Sweep-based: also remove any installed extension subdirectory not in the current bundle,
+  // even if it was never tracked in the manifest (e.g. installed by a pre-manifest version).
+  try {
+    if (existsSync(extensionsDir)) {
+      for (const e of readdirSync(extensionsDir, { withFileTypes: true })) {
+        if (e.isDirectory()) removeDirIfStale(e.name)
+      }
+    }
+  } catch { /* non-fatal */ }
+
   // Always remove known stale files regardless of manifest state.
   // These were installed by pre-manifest versions so they may not appear in
   // installedExtensionRootFiles even when a manifest exists.
diff --git a/src/tests/resource-loader.test.ts b/src/tests/resource-loader.test.ts
index 637b9088a..03bbd5db2 100644
--- a/src/tests/resource-loader.test.ts
+++ b/src/tests/resource-loader.test.ts
@@ -160,3 +160,49 @@ test("initResources prunes stale top-level extension siblings next to bundled co
   assert.equal(existsSync(staleSiblingPath), false, "stale top-level sibling should be removed during sync");
   assert.equal(existsSync(bundledPath), true, "bundled extension should remain after cleanup");
 });
+
+test("pruneRemovedBundledExtensions removes stale subdirectory extensions not in current bundle", async () => {
+  const { initResources } = await import("../resource-loader.ts");
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-resource-loader-prune-dirs-"));
+  const fakeAgentDir = join(tmp, "agent");
+
+  try {
+    // First sync — seeds the agent dir and writes the manifest.
+    initResources(fakeAgentDir);
+
+    // Simulate a stale subdirectory extension left from a previous GSD version.
+    // This mirrors the mcporter scenario: it was bundled before, synced to
+    // ~/.gsd/agent/extensions/, then removed from the bundle in a newer version.
+    const staleExtDir = join(fakeAgentDir, "extensions", "mcporter");
+    mkdirSync(staleExtDir, { recursive: true });
+    writeFileSync(join(staleExtDir, "index.ts"), 'export default { name: "mcporter" };\n');
+    assert.equal(existsSync(staleExtDir), true, "stale subdir extension should exist before prune");
+
+    // Read the manifest to verify subdirectory extensions are tracked.
+    const manifestPath = join(fakeAgentDir, "managed-resources.json");
+    const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
+
+    // The manifest must record installed extension directories so the pruner
+    // can detect when one has been removed from the bundle.
+    assert.ok(
+      Array.isArray(manifest.installedExtensionDirs),
+      "manifest should contain installedExtensionDirs array",
+    );
+
+    // Bump the manifest version to force a re-sync (simulates upgrading GSD).
+    manifest.gsdVersion = "0.0.0-force-resync";
+    manifest.contentHash = "0000000000000000";
+    writeFileSync(manifestPath, JSON.stringify(manifest));
+
+    // Second sync — the bundle no longer contains mcporter/, so it must be pruned.
+    initResources(fakeAgentDir);
+
+    assert.equal(
+      existsSync(staleExtDir),
+      false,
+      "stale subdirectory extension (mcporter/) should be pruned after upgrade",
+    );
+  } finally {
+    rmSync(tmp, { recursive: true, force: true });
+  }
+});