Application has the following file structure:

/ - server root
/framework - FW root
/framework/3rd/ (...) for 3rd party libraries
/framework/class/ (...) for basic classes
/framework/controllers/ (...) for common controllers
/framework/pages/ (...) common pages goes here (e.g. 404.html)
/framework/temp/ (...) for temp data
/framework/framework.php - main include file

...

/public_html/site1/class/ (...) site-specific classes
/public_html/site1/controllers/ (...) site-specific controllers
/public_html/site1/pages/ (...) site-specific HTML pages / templates
/public_html/site1/images/ (...) images (accessed directly due to .htaccess rules)
/public_html/site1/layout/ (...) other site-specific layout files (css, js...)
/public_html/site1/.htaccess - basic rules for HTTP request redirecting
/public_html/site1/config.ini - site configuration (appids, DB access etc.)
/public_html/site1/index.php - the site front controller - includes "framework.php" and does some site-specific actions, if needed

The same structure can has site2, site3, another-site...