Package visibility index reforms

[liach]

Since we now have access widener, for the package visibility index, instead of joining classes into disjoint unions, we should track package-access entry references and see if they are fulfilled by the mapping (either raise the referenced entry's access level or check if they are mapped into the same package).

In addition, we can consider if we should always run this visibility index with jar index or only run it manually, as now it's always run with the jar index but almost never used (only used from enigma cli, yarn mapping check)

In addition, we should probably enforce same-package rule for nests: if a nest member is not in the same runtime package as its host, it's automatically on its own (see jvms 5.4.4, access control).