Why not just change the DocumentRoot directive in the configuration so that it points to the right place?
What do you mean by "hundreds of files"? Have you "included" files and used the full path in the reference? An editor such as EditPlus3 could do a find and replace on all of your files in minutes. However, the server path for PHP includes (if that is what it is) should have been defined in a variable or set as a configuration line in the config file or in .htaccess.