Minor fixes on URI permission methods.

- clearGrantedUriPermissions() was clearing all permissions, including those
  where the app was the source of the permission.
- clearGrantedUriPermissions() was not thread safe.
- takePersistableUriPermission() was creating an extra object.

Bug: 63720392
Test: manual verification

Change-Id: I57a7b2c40b0e258f373f50badbb376daad3ca2d0