Stop showing disabled apps in the app launcher and shelf greyed out.

These apps can still be run, they just need to go through an enable
flow.

BUG=321502, 286479
TEST=Check that apps which have been updated in the store to have new
permissions can be launched properly, and are not shown greyed out.

Review URL: https://codereview.chromium.org/81333004

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@236736 0039d316-1c4b-4281-b951-d872f2087c98
SVN changes up to revision 236736
Disable PnaclHeaderTest.TestHasPnaclHeader.

The test is still flaky, so the change in r235824 didn't help.

NOTRY=True
BUG=315328
TBR=jvoung@chromium.org

Review URL: https://codereview.chromium.org/83103002

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@236737 0039d316-1c4b-4281-b951-d872f2087c98
SVN changes up to revision 236737