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

chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json

Index: chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json
diff --git a/chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json b/chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json
index 799ba270683d42d441883256435aaac0178a2f6a..e3d86d2f5297bc79c045f86a235ba1aea2e070dc 100644
--- a/chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json
+++ b/chrome/test/data/extensions/platform_apps/messaging/app2/manifest.json
@@ -2,7 +2,6 @@
   "key": "AAAAB3NzaC1yc2EAAAADAQABAAABAQDbh1pj7Q+vZzotbfPfe1Q4AIeJc3gU1xhTSMtjB0UZH+G3ckScJYTnFCTkFAn/mEOtn7e+SZ9rhDf4k6X7Qf6BzK3PLNn3+2Hb/F0NC57hiWI2UyhXY2dl2ry6VENkuyo1QpEMGH5FB5tC2rcuivG8ipBbUWLoQLMbegUdOLXoNK4tGvKwlGa1B0QPAMIkEw3ZlerckC8e+tWC38WvHxy1EM5VeK8k4GcrDEltoVByprTe/8VTzvEsFFYljpIzbSTi6mKOhY2sdl0EfCpXT4dSCeSe81O8liMU1yYKBQCbzguASV7yzZMX08tb96MOpx0NYbYXt03Zyj3xlbep5n4l",
   "name": "Messaging Test App 2",
   "version": "0.5",
-  "permissions": [ "app.runtime" ],

[not at google - send to devlin, 2013/10/28 22:42:50]

The test is that installing this app results in no warnings, which now that this
isn't a permission, isn't the case.

This change is still backwards compatible - these are install warnings, not
errors.

[rpaquay, 2013/10/28 22:54:45]

Shouldn't we also remove this permission from 
chrome/test/data/extensions/platform_apps/messaging/app1/manifest.json
chrome/test/ext_auto/auto_provider/manifest.json
?

[not at google - send to devlin, 2013/10/28 22:57:15]

Yes. Thanks.

[rpaquay, 2013/10/28 23:01:31]

Do another quick search, and found "app.window" here:

chrome/test/ext_auto/auto_provider/manifest.json
chrome/test/data/extensions/platform_apps/apps_only/manifest.json

I assume they should be remove too.

   "app": {
     "background": {
       "scripts": ["background.js"]