Ok, so there are a couple of things already in the works for the next update. One is that Homebridge and Homebridge-Indigo will be part of the plugin, thus taking care of the need to install anything on your computer. Second, the aforementioned installation will allow for multiple installations on a single computer, eliminating the need to support running HB on remote computers entirely since this now sufficiently addresses the 100 device limit. The other new feature will be the ability to add your own platforms and/or accessories to each server instance for those cases where you are using additional HB plugins other than HB-Indigo and HB-Camera-FFMpeg (camera is also included in the default build).
Why? For one, and this has always been an important part of getting this finished, there needs to be a really simple way for new folks to get Homebridge up and running without dropping to a shell and installing it all by hand, this takes care of it. Also, until now if you wanted to break the 100 device limit you had to run HB on different computers, each computer giving you another 100 devices - now one computer can support ALL of your devices. Finally, I believe there is a necessity to be able to manipulate the config.json as you need in order to support your other plugins and there's no way I'm going to build in support for 400 (and growing) currently available NPM plugins!
Everyone currently running HBB has the "original" installation of Homebridge, that is that they followed Webdecks instructions to get it up and running. New users will just default to using the built-in HBB version of Homebridge (which is identical by the way to what you have now).
I have all sorts of ways to go on this and am curious what the community preferences are in regards to this new version of HBB that has HB in it - migrate the current HB config into the new one, run both side-by-side, ability to use the old version and ignore the new one... What would you like to see?