Update more extension manifests to manifest_version 2

chrome/test/data/extensions/app3/manifest.json

 {
   "name": "Test App 3",
   "version": "1",
+  "manifest_version": 2,
   "app": {
     "urls": [
       "http://www.example.com/path1/should_overlap",
       "http://www.example.com/path5"
     ],
     "launch": {
       "web_url": "http://www.example.com/path5/foo.html"
     }
   }
 }