Git - multi content roots

Hi,

I'm not so firm in Git - but I tryed to commit / push my PHP-projekt to bitbucket.org.

Normaly thats no problem. But her I have a project with 2 content-roots.

One Directory is the htdocs (here are all files that should be under Document-Root from Server.

Than there is a directory 'closed' - somerwhere else on the server (here it is in the same directory in wich the htdocs directory is).

So - how can I manage this with Intellij an GIT?

I want them all to push into one project on bitbucket (git) is it possible?

cu