Multiple application folder in CI

If you would like to share a common CodeIgniter installation to manage several different applications simply put all of the directories located inside your application folder into their own sub-folder.

For example, let's say you want to create two applications, "foo" and "bar". You could structure your application folders like this:
applications/foo/
applications/foo/config/
applications/foo/controllers/
applications/foo/errors/
applications/foo/libraries/
applications/foo/models/
applications/foo/views/
applications/bar/
applications/bar/config/
applications/bar/controllers/
applications/bar/errors/
applications/bar/libraries/
applications/bar/models/
applications/bar/views/



Ref: https://ellislab.com/codeigniter/user-gu..._apps.html