diff --git a/extensions/pi-config/index.ts b/extensions/pi-config/index.ts
index 85c9b75..28ae71c 100644
--- a/extensions/pi-config/index.ts
+++ b/extensions/pi-config/index.ts
@@ -115,12 +115,16 @@ function saveSettings(cwd: string, settings: PiSettings): void {
   fs.writeFileSync(projectSettingsPath(cwd), JSON.stringify(settings, null, 2) + "\n");
 }
 
-/** Ensure the agents package entry exists, creating it if missing */
+/** Ensure the agents package entry exists, creating it if missing. Always ensures extensions/skills arrays exist to block auto-discovery. */
 function ensureAgentsPackage(settings: PiSettings): PackageFilter {
   const existing = findAgentsPackage(settings);
-  if (existing) return existing;
+  if (existing) {
+    existing.extensions ??= [];
+    existing.skills ??= [];
+    return existing;
+  }
 
-  const entry: PackageFilter = { source: AGENTS_DIR };
+  const entry: PackageFilter = { source: AGENTS_DIR, extensions: [], skills: [] };
   const pkgs = settings.packages ?? [];
   pkgs.push(entry);
   settings.packages = pkgs;