The Apollo system seems to be non-standard in a number of ways that make it difficult for a first time installer/developer/user like me:
It can be very convenient to install an application once in one location on one filesystem and then share that application with all users and all computers that have access to that shared filesytem so anyone anywhere on your network can run the application without bothering or risking to download and install it personally. This should be possible with Apollo because it is free software in every sense but there does not seem to be a separation between the code (read-only) and the personal configuration and data which must be writeable ? The restricted one-user one-installation model is not efficient and is forced on Microsoft Windows users who might think it is normal and mistakenly think that it is therefore good. The personalisation file "ensj.tiers" should be in a users home directory tree, and the example data can be shared whilst annotations can be shared or personal.
The source code comes with a non-standard package name starting with "apollo" instead of a top-level domain name like com or org which is the convention used by all other Java programmers. Or, at least the CVS download comes with a batch file that looks for such a class:
Exception in thread "main" java.lang.NoClassDefFoundError: apollo/main/Apollo
Caused by: java.lang.ClassNotFoundException: apollo.main.Apollo
and the sourceforge links complain when the user arrives without having previously logged in to source forge
Thanks for sharing, I will put other, more specific, bug reports separately.