Dankness...great job...(re-installed)
It now works out-of-the-box.
I would modify the installation instructions:
- In case of a fresh installation, you don't need to upload the treemenu.php file as the .module file will try to recreate it and vBA would ask if you want to overwrite, rename etc.

Simply import the module and upload the clientscript directory for fresh installation of the hack on vBA 3.0RC2.
Also, the URL replacement is now working when you click on the links.
Keep up the great work...