I have been carrying out a couple of site develops recently, and that i really hate getting the main folder so cluttered. I'm not going anything influenced around the idea, like Search engine optimization, wordpress plugin/theme complications, etc.
The physical locations of the files and also the Web addresses to gain access to assets are realistically distinct. Place the the application anywhere you would like and employ your internet servers configuration directives for everyone them from the URL.
PHP usually "file based" system. Each URL executes b .perl file (usually) so the distinction above will get just a little blurred.
Wordpress is offered from the root directory (reason for installation) and all sorts of situations are acquired after that so sub sites aren't an problem.