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

chrome/common/extensions/api/_permission_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.
 
 {
   "activeTab": {
     "channel": "stable",
@@ skipping 11 matching lines @@
   },
   "adview": {
     "channel": "dev",
     "extension_types": ["platform_app"]
   },
   "alarms": {
     "channel": "stable",
     "extension_types": ["extension", "legacy_packaged_app", "platform_app"],
     "min_manifest_version": 2
   },
-  "app.runtime": {
-    "channel": "stable",
-    "extension_types": ["platform_app"]
-  },
-  "app.window": {
-    "channel": "stable",
-    "extension_types": ["platform_app"]
-  },
   "audio": [
     {
       "channel": "dev",
       "extension_types": ["platform_app"]
     },
     {
       "channel": "stable",
       "extension_types": ["platform_app"],
       "whitelist": [
         "8C3741E3AF0B93B6E8E0DDD499BB0B74839EA578",
@@ skipping 786 matching lines @@
     // Only allowed for whitelisted extensions until all the caveats are
     // addressed. Tracked in crbug/285151.
     "channel": "stable",
     "extension_types": ["extension"],
     "location": "component",
     "whitelist": [
       "mfffpogegjflfpflabcdkioaeobkgjik"  // GAIA Component Extension
     ]
   }]
 }