Installing third party app

[eluser]peter222[/eluser]
I think about any application, not necessarily in MVC and CI. For example phpbb3 and others. I know instructions and know how to install it as standalone appliacation. As standalone I put it in own folder, run installer and that's all. Problem is when I try to run installer as a part of existing CI application. As I wrote before, when try to put it just in CI subdirectory, I can't call it by mysite.com/app_folder (because CI think I want to run controller). So, what can I install any external application and view it just as one of items in my existing CI App menu?