Update PackageSetting flags when updating

Commit 5e03e2ca moved from
PacakgeParser.Package to PackageSetting which revealed that we weren't
updating the pkgFlags when replacing an existing application.

Add flags to PackageSetting so that deletion of the package later succeeds.

Change-Id: I2e0d4e07da31f48b68601f3f3240966b6e17dbdf