It sounds like you're looking to gradually make less use of CodeIgniter's (CI) routing as your angular application grows. This is not difficult but requires a lot of detail. Which method will work depends on your project structure. Note: I removed index.php from Code Igniter URLs, so the paths below may be different than default.
1) CodeIgniter installed in root
If CI is installed on the root of your server, you can create a folder within CI (for instance I have an "ng" folder). Your project will look like:
/controllers
/models
/ng
(etc)
/index.php (code igniter index file)
place an .htaccess file within /ng with the following:
Order allow, deny
Allow from all
This allows the files within /ng to be directly accessed, rather than sending those requests back through CI's routing system. For example you can load this directly now:
example.com/ng/partials/angular-view.html
The main web page will still be created by CodeIgniter, but it can now include Angular assets, such as partial views, etc. Eventually you can replace most of what CodeIgniter is doing by just returning a simple page, and having Angular load partial views from /ng like it's designed for.
This method is nice because CodeIgniter can control whether that initial page is loaded at all (via some user authentication code in your CI controller). If user isn't logged in, they are redirected and never see the Angular app.
2) CodeIgniter in Directory
If CI is installed in a directory, such as example.com/myapp/(code igniter) you can simply create a directory next to it, example.com/myappNg/
/myapp/
/myapp/controllers/
/myapp/models/
/myapp/(etc)
/myapp/index.php (code igniter index file)
/myappNg/
/myappNg/partials/
/myappNg/js/
/myappNg/(etc)
Now in your Angular application, you can request resources from CI by making paths relative to the domain root, rather than relative to the Angular app. For instance, in Angular, you will no longer request a partial view from the Angular folder partials/angular-view.html, rather you'll want to request views from CI /myapp/someResource. Note the leading /. "someResource" can return an html document, or JSON or whatever you're doing with Code Igniter in the first place.
Eventually you can replace the number of paths which reference /myapp/. Once you no longer use CI for anything, you can simply place your Angular index.html in /myapp/ and it will continue to reference your paths at /myappNg/.
TL;DR Make your Angular app fully available and decouple it from CodeIgniter. Gradually move toward using Angular partial views and other JSON sources instead of linking to CodeIgniter pages. Eventually replace your CodeIgniter endpoint with an HTML file which bootstraps Angular.
