fix(coding-agent): respect package.json pi.extensions manifest in settings extensions paths

collectAutoExtensionEntries now checks if the directory itself has a
package.json with pi.extensions (or index.ts) before scanning children.
This fixes duplicate extension loading when a manifest-aware directory
is specified directly in settings.json extensions array.

Fixes #1274

packages/coding-agent/src/core/package-manager.ts

@@ -402,6 +402,13 @@ function collectAutoExtensionEntries(dir: string): string[] {
 	const entries: string[] = [];
 	if (!existsSync(dir)) return entries;
 
+	// First check if this directory itself has explicit extension entries (package.json or index)
+	const rootEntries = resolveExtensionEntries(dir);
+	if (rootEntries) {
+		return rootEntries;
+	}
+
+	// Otherwise, discover extensions from directory contents
 	const ig = ignore();
 	addIgnoreRules(ig, dir, dir);