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

extensions/common/permissions/api_permission.h

 // Copyright 2013 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.
 
 #ifndef EXTENSIONS_COMMON_PERMISSIONS_API_PERMISSION_H_
 #define EXTENSIONS_COMMON_PERMISSIONS_API_PERMISSION_H_
 
 #include <map>
 #include <set>
 #include <string>
@@ skipping 21 matching lines @@
   enum ID {
     // Error codes.
     kInvalid = -2,
     kUnknown = -1,
 
     // Real permissions.
     kActiveTab,
     kActivityLogPrivate,
     kAdView,
     kAlarms,
-    kAppCurrentWindowInternal,
-    kAppRuntime,
-    kAppWindow,
     kAudio,
     kAudioCapture,
     kAutoTestPrivate,
     kBackground,
     kBluetooth,
     kBookmark,
     kBookmarkManagerPrivate,
     kBrailleDisplayPrivate,
     kBrowsingData,
     kCast,
@@ skipping 269 matching lines @@
   const char* const name_;
   const int flags_;
   const int l10n_message_id_;
   const PermissionMessage::ID message_id_;
   const APIPermissionConstructor api_permission_constructor_;
 };
 
 }  // namespace extensions
 
 #endif  // EXTENSIONS_COMMON_PERMISSIONS_API_PERMISSION_H_