Move files to public directory.

Move all the publically accessible files to a directory named "/public" as this will be the new webroot, so that the yiiframework and application files will not be accessible to the web.
Remove htaccess.

Removed the htaccess file from the protected application directory as it is no longer needed now the directory is not in the webroot.
Rename app folder.

Rename the application directory "protected/" to "flowgui/". It is much better at describing what the application directory is from first-glances.
Configure paths.

Configure the paths to the Yii Framework and application configuration now that the webroot has moved.
Merge branch 'feature/webroot' into develop