Short, non-official answer is ‘I don’t know’, but I haven’t been pondering it too hard because I’m waiting for EE 2.0 to come out- which will be written on top of CI. (Is that what your existing apps are using?)
Anyway, been poking around CI and trying to get up to speed on it- and the MVC logic. But until 2.0 comes out and I get to see how EE based modules/plugins/etc. will work, I’m not poking too hard.
That make a lick of sense?
ETA- must read TITLE. Yes, you are using CI! Heh. Yep, right now I don’t quite grok how it will all work and when it will be best to write custom code as an EE plugin/etc. and when to write it as a pure CI ap- which I have no doubt will sometimes be the best option. From what I’ve seen- should be able to run multiple applications from CI no problem- with EE being a single application. Anyway, that’s just me, guessing a bit and not as up on CI as I should be.