Unfortunately the short answer is there is no way of doing nested folders with the current version of Message Saver. While the following suggestion will not help to replicate the project folder structure, you can use a Find (QuickFinder) to dislay all items within the project folders, select all items in the Find Results listing, and then save them to a single disk folder.
We have recently released Advansys Archive To Go – Mailbox Exporter for GroupWise. This solution exports a full GroupWise mailbox to disk (FML format) and preserves the complete GroupWise folder structure as a portable archive. A future release will include the capability to select only the folders you wish to export, thus providing the capability to create a portable archive of a complete or partial mailbox.
Thank you for your feedback and we will include your requirements when reviewing our future product plans.