Update package use info when the app data is updated

- clear usesByOtherApps flag when the package is updated
- delete secondary dex usage data when the app data is destroyed

Test: runtest -x .../PackageDexUsageTests.java
      runtest -x .../DexManagerTests.java
Bug: 32871170
Bug: 35381405

Change-Id: I3a249b9e8680e745fa678c7ce61b4ae764078fb9