These directions are thought for techies that already have experience with Linux and/or Unix. FHS is a key topic in regards to this subject. Wether you are used to Linux or not I recommend that people get familiar with the FHS standard (Filesystem Hierarchy Standard) to know the environment being used. Naturally there are many nuances in regards to setting up and deploying an application server successfully in different environments and for differing goals but those are a matter of soliciting consulting help from us. We have after all been working on this for quite some time and have successfully deployed production services with this technology.

To securely copy files back and forth it's best to use SCP (Secure Copy). Secure copy uses the secure shell protocol (ssh) and is virtually installed by default on all Unix related systems.  Many ssh and scp programs have been built for Windows and probably the best known and popular ones are Putty and its sybling pscp (also look up putty.org for other good Unix related Open Source tools for Windows or if the link is outdated).