Good way to manage php software

I have several web sites on my server and have some problem with installing and upgrading php (mostly, but not only) software using ports. For example let's see about Joomla.

To install joomla I need to install Apache, PHP, database and joomla itself from ports tree. Later I follow instructions from joomla port to add joomla as alias. But after finishing insallation process, I got message to remove installation directory which is located in /usr/local/www/joomla by default. Disabling this directory with HTTP will not work.

It is not problem for manual installation without using ports tree for joomla, but become headache when you manage several sites and minimize risks. After copying joomla code I'll have no information if my sites are vulnerable.

Why not to link directories? supporting links some harder than copy files.

So, how should I setup joomla, to have portaudit(8) notifications about this software? How should I update vulnerable versions to patched? How should I serve joomla installations without copying files and using these from installed from ports?

Trac, Django, Zope and some other python software have difference between installed software and site instance, so there are no same headaches. Are there any same solution?
 
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