RewriteEngine On

RewriteBase /reference/
RewriteCond %{ENV:REDIRECT_SURI} !^$
RewriteRule (.*) - [L]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^(.+[^/])$ $1/ [L]

RewriteRule ^$ site/index.php [E=SURI:1,L]
RewriteRule ^(doc|timeline|admin)/?$ site/$1/index.php [E=SURI:1,L]
RewriteRule ^doc/functions/?$ site/doc/functions/index.php [E=SURI:1,L]
RewriteRule ^doc/functions/list/? site/doc/functions/list/item.php [E=SURI:1,L]
RewriteRule ^doc/functions/detail/? site/doc/functions/detail/item.php [E=SURI:1,L]