"With Habari you must have a folder and the plugin file must share that name, using the format [folder name].plugin.php. This is important as it is part of the system that finds and runs plugins."
Actaully that is not true. You can name the folder anything you want and the plugin file [anything].plugin.php. So you do not need to make them match.
And this is a great post! Thanks for doing it. And nice idea about the plugin wizard (can you make it use tabs instead of spaces ;) ).