Custom (user-created) packages.

Password store, and passwords.

Configuration files for Integration Server, hosted products such as Trading Networks, and hosted Wm packages that are also hosted on the new Integration Server.

JDBC connection pool configurations, database drivers, and functional aliases.

Starting in 9.5, custom (user-created) jar files.

JAAS configuration files.

Java Service Wrapper customizations you made in the old custom_wrapper.conf files, including #include directives and comments (but not associated properties).