webapps directory structure

On other servers when setting up websites for, I've typically setup the folders as follows:

 - httpdroot 
 -+ app1
    -+ docs     // actual apache document root for app1
      -+ images
      -+ scripts
      -+ css
    -+ includes    // php includes folder - not inside app1 document root
    -+ logs

On webfaction, these are scattered, at least the log files are completely separate and it took me a while to find them. I try to put my includes folders elsewhere for security reasons, but this makes it hard to manage because everything gets scattered.

It's especially a nuisance when I try to use Git to manage and deploy sites - unless I put everything in the same folder.

What does everybody else do here? Just put the includes folders into the document tree and rely on .htaccess directives to keep people out of them? Is there something I missed in the control panel that would let me force the document root to be ~/webapps/app1/docs/ instead of ~/webapps/app1 ?