The new system will allow Krang to mature into a true application development platform. Addons will be installed into their own space under addons/. This has two important advantages: 1) it will keep addons from accidently or purposefully overwriting Krang source files (and vice-versa) and 2) addons can be developed in-place under version control.
Fixing these two issues should make developing add-ons a lot more pleasant. But the new design doesn't stop there - it also brings Krangs build system to addons so they can come with their own dependencies. A new class factory system will allow add-ons to selectively extend core Krang classes without needing to alter Krang's code. Finally, Krang's left-nav area will be modularized so add-ons can register new entries without having to completely override the navigation templates.
The new system should land in Krang v1.103 sometime later this week. I'm off on a branch for now so v1.102 can get out the door without more QA.