Only grant runtime permissions to special components.

Now runtime permissions are granted only to components that are
part of the system or perform special system operations. For
exmple, the shell UID gets its runtime permissions granted by
default and the default phone app gets the phone permissions
granted by default.

bug:21764803

Change-Id: If8b8cadbd1980ffe7a6fc15bbb5f54a425f6e8f9