Project organisation for Drupal

I use multi-site Drupal environment, but I work with every site separately.

I'd like to attach Drupal core as a Library or something like extended sources, leaving only site files in project. Problem is that sites directory is located inside Drupal core directory

www - I want PhpStorm to index this directory as an library, excluding 'sites' directory if possible
          site02 - And this is a project directory

I don't want to add all www as a project, as Drupal core files and files of other projects are not supposed to be edited when working on some project, and there would be a mess in Project Explorer
Is there a way of working with this directory structure in a nice way?

I use latest 2.0 EAP version at the moment.
P. S. Forum visual editor works incorrectly in Opera 10.70

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I would do it as follows. Add Drupal as library as mentioned. Then under Tools > Deployment set it up so that the project goes in the site folder of our sites folder when you run it. I think this should work...

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If working with Drupal you should also create a global.php file so you can reference global variables with "ctrl + space"x2

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Thing is I cant find where to add External Libraries in EAP 2.0 version. It's confusing.
I can add `context root` in Project settings, but actually it wont allow me to add directory containing project directory anyway.
Using www as project root and configuring Deployment settings wont solve the problem of code mess and indexing of all other site directories - there are way too many of them. I don't want neither Drupal core modules neither other site directories be indexed and shown in navigation.


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