Why are there so many index.php files in my WordPress installation?

There are a LOT of index.php files sprinkled throughout your WordPress site. Each one is important and performs a particular function. If your curiosity spurs you to look at these using your text editor, you'll notice that a good many contain only one comment:

// Silence is golden

These particular index.php files exist to obscure the contents of the directory that it belongs to, so that by visiting the directory directly in the browser (ex: mysite.com/wp-content/) - you would get a blank page, rather than a list of all the directory items. 

The index.php file in the root of your installation contains code that is necessary to load and initialize all the files that together will serve up the page you have requested in the browser. (Don't touch this one!)

The index.php file in the root of your theme is the default template file that will display your site content should a more specific theme file not be available. In your WordPress class, when we ask that you edit your index.php file, this is the file that we are referring to.