Every page generated by MODX begins with the index.php file, and the Manager pages begin with the /manager/index.php file. Everything else is done by including the other .php files as they are needed.
Revolution is designed in such a way that the core directory and all of its files and subdirectories do not need to be in the web root. There are three config files to let MODX know where its core is located.
The /assets/ and /manager/ directories do need to be in the web root, since they all contain files such as images and .js files that a browser needs to be able to access. However, their names can be changed. The config.inc.php file has the definitions for these directories.