Fix issue #5446988: WindowManager warns BOOT TIMEOUT,...

...dev.bootcomplete flags is set before boot animation is out

Also:

- Fix crash in recent apps if the intent for an old app didn't
happen to have the new task flag set.
- Fix issue where a crash in system UI would cause the crash
dialog to be displayed below it, effectively locking the UI.  Now
the crash dialog for persistent processes is shown above everything
else.

Change-Id: I0312001a92beeae5f644c7c3e5c5e19f6716df36