Usually the index file is just the basics. But it does depends on what your doing.

A CMS is a very large project and how they set it up will vary greatly from a smaller project.

Generally I use the index file to set the base HTML layout of a site. It will include the CSS, Javascript, PHP pages. These pages of code then determine what content will be displayed, and how it will be displayed, in the different sections of the index page.

So while my index page may be less than 200 lines of code usually I have 7 to 15 other pages (sometimes more) of code that are included inside of it and they can be anywhere form 200 to 1000 lines of code that determine what content is displayed in the various sections of the index page.

Unless the whole site is 5 or so pages I usually have no content displayed with just the index page.