Use _api_features checks for app.runtime and app.window instead of permissions.

Eliminate the corresponding dummy permissions.

BUG=310707
TBR=achuith@chromium.org

Review URL: https://codereview.chromium.org/131103012

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@246494 0039d316-1c4b-4281-b951-d872f2087c98
SVN changes up to revision 246494