Sadly CodeIgniter 2.0-dev has not brought us any sort of modular/HMVC system, but luckily Modular Separation works for this new "version" with two minor tweaks.
The fix was worked out a few hours after the CodeIgniter 2.0 dev code was released but I was hoping wiredesignz would incorporate and re-post. Sadly the man has other commitments to attend to, so I have released the patched version.
I will use this fork to work on some cool new CodeIgniter 2.0 related features such as supporting Packages as well as the existing custom "module location" array.
_ Note: In no way is this intended as theft of wiredesignz work. He is a brilliant developer who I have a great deal of respect for, so please notice his name is still on every file with only "@modified Phil Sturgeon" added in. I have patched his work._
_ Update: There was some confusion in this post with my wording. CodeIgniter 2.0 is not officially released yet, I am talking about the development code. DO NOT use CodeIgniter 2.0 on any live sites just yet, I will post an update when I feel confident enough to run CodeIgniter 2.0 on my live sites.