Ensure package check is run for java_library in APEX

Package checks were not being run for java libraries that were in an
APEX and not on the platform. This change fixes that and updates the
script to report all failing classes to make it easier to update the
list of packages.

Test: m java
Bug: 157633658
Change-Id: I28044e08d3a40e9f3464bb2158ef6a28d57264d1