The most important one is the ability to supply a fileManager. While
JShell uses runtime platform supplied Filemanager, the user code may
target a different JDK (patch release, for example); I need the ability
to analyse and compile against the exact runtime used afterwards to run
the code.

Similar to that is a change in JdiInitiator; again, the calling IDE
needs to specify "home" property in order to invoke VM from the correct
JDK installation. Running / testing user applications on specific patch
releases may be very important.