With many web sites, if you use as the URL, for example, www.example.com/pages/main/index.php, you are accessing the file 'index.php' in the folder 'main' in the folder 'pages.' How would you instead program the web site so that when the URL www.example.com/pages/main/index.php is entered, the primary web application (stored directly in the site root directory) knows that this URL was entered and can serve the proper web page? This is a somewwhat general question, but it should have specific code answers and can certainly be answered, and as such was asked. The web application would be written in PHP.
This can be solved with .htaccess and rewrite rules.
See .htaccess rewrite to redirect root URL to subdirectory or http://coding.smashingmagazine.com/2011/11/02/introduction-to-url-rewriting/
Note that mod_rewrite should be enabled in apache settings