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Default Page for CodeIgniter Site/WordPress in Sub Directory

1:44 pm on Oct 9, 2013 (gmt 0)

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I'm the developer for a website with Analytics already set up and the Default Page is set to index.php. This is because it is built with the PHP Framework CodeIgniter.

I'm confused about and have questions about a few things...

GA shows /index.php as the main page, then for about 10% of the results of inner pages it will append index.php to the end of the URL and nothing at the end of the rest of them (no trailing slash). Why is that?

And my main concern, WordPress is installed in another directory (/articles) and GA shows and /index.php on every page for WordPress. Of course, those pages come up as 404s if I put them in my browser with the /index.php. Are visitors seeing those 404 pages or is GA just adding that /index.php because it's set as the Default Page?

What's the best way for me to set this up in GA under these circumstances?