Fix visibility was gone after updating

System grants implicit visibility when the Uri permission is granted.
But, all the visibility rules would be cleared when package updating.
Since the implict visibility doesn't come from manifest, we cannot
restore it via recompuating visibility. This solution is similar to
how UriGrantsManagerService handles the granted Uri permissions when
packagea updated. We keep them unchanged instead of clearing them.

Bug: 161912313
Test: atest AppsFilterTest
Test: atest AppEnumerationTests
Test: atest UriGrantsManagerServiceTest
Test: manually use test APKs on buganizer to verify
Change-Id: I3026e06574f78c15dbf60c74db126679c677adb1