diff --git a/tools/installer/core/manifest-generator.js b/tools/installer/core/manifest-generator.js
index 477142888..df8484d8b 100644
--- a/tools/installer/core/manifest-generator.js
+++ b/tools/installer/core/manifest-generator.js
@@ -193,11 +193,13 @@ class ManifestGenerator {
           }
         }
 
-        // Recurse into subdirectories
-        for (const entry of entries) {
-          if (!entry.isDirectory()) continue;
-          if (entry.name.startsWith('.') || entry.name.startsWith('_')) continue;
-          await walk(path.join(dir, entry.name));
+        // Recurse into subdirectories — but not inside a discovered skill
+        if (!skillMeta) {
+          for (const entry of entries) {
+            if (!entry.isDirectory()) continue;
+            if (entry.name.startsWith('.') || entry.name.startsWith('_')) continue;
+            await walk(path.join(dir, entry.name));
+          }
         }
       };
 
diff --git a/tools/installer/fs-native.js b/tools/installer/fs-native.js
index b6a4abfa5..1d84af98a 100644
--- a/tools/installer/fs-native.js
+++ b/tools/installer/fs-native.js
@@ -82,7 +82,9 @@ module.exports = {
   stat: fsp.stat,
   readdir: fsp.readdir,
   access: fsp.access,
+  realpath: fsp.realpath,
   rename: fsp.rename,
+  rmdir: fsp.rmdir,
   unlink: fsp.unlink,
   chmod: fsp.chmod,
   mkdir: fsp.mkdir,
@@ -103,6 +105,9 @@ module.exports = {
   existsSync: fs.existsSync.bind(fs),
   readFileSync: fs.readFileSync.bind(fs),
   writeFileSync: fs.writeFileSync.bind(fs),
+  statSync: fs.statSync.bind(fs),
+  accessSync: fs.accessSync.bind(fs),
+  readdirSync: fs.readdirSync.bind(fs),
   createReadStream: fs.createReadStream.bind(fs),
   pathExistsSync: fs.existsSync.bind(fs),