Make app APIs implicit within _api_features.json not _permission_features.json.

chrome/common/extensions/api/_api_features.json

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 // See c/c/e/features/* to understand this file, in particular feature.h,
 // simple_feature.h, and base_feature_provider.h.
 
 {
   "activityLogPrivate": {
     "dependencies": ["permission:activityLogPrivate"],
@@ skipping 11 matching lines @@
     "channel": "stable",
     "extension_types": ["hosted_app", "extension", "legacy_packaged_app"],
     "contexts": [
       "blessed_extension", "unblessed_extension", "content_script", "web_page"
     ],
     "matches": [
       "http://*/*", "https://*/*", "chrome-extension://*/*", "file://*/*"
     ]
   },
   "app.runtime": {
-    "noparent": true,
+    "channel": "stable",
     "contexts": ["blessed_extension"],
-    "dependencies": ["permission:app.runtime"]
+    "extension_types": ["platform_app"],
+    "noparent": true
   },
   "app.window": {
-    "noparent": true,
+    "channel": "stable",
     "contexts": ["blessed_extension"],
-    "dependencies": ["permission:app.window"]
+    "extension_types": ["platform_app"],
+    "noparent": true
   },
   "app.currentWindowInternal": {
     "noparent": true,
     "internal": true,
     "channel": "stable",
     "contexts": ["blessed_extension", "unblessed_extension", "content_script"]
   },
   "app.currentWindowInternal.setAlwaysOnTop": {
     "channel": "dev",
     "contexts": ["blessed_extension", "unblessed_extension", "content_script"]
@@ skipping 665 matching lines @@
     "internal": true,
     "channel": "stable",
     "dependencies": ["permission:webview"],
     "contexts": ["blessed_extension"]
   },
   "windows": {
     "dependencies": ["api:tabs"],
     "contexts": ["blessed_extension"]
   }
 }