Fourth batch of permission in-process API refactoring.

- Replaced resetAllRuntimePermissions() with directly calling
  resetRuntimePermissions() for all packages and save one API.
- Moved canPropagatePermissionToInstantApp() back into
  InstantAppRegistry, as it's up to the instant app managing component
  to determine what should be propagated.
- Renamed systemReady() to onSystemReady().

Bug: 158736025
Test: presubmit
Change-Id: I124a35eeead99c3124636d3b63b389ff9c3eacfd