Eclipse - Exclude root directory from git repository?

I'm trying to setup a git repository for my Eclipse project using EGit. However, I'm having trouble excluding the root/project directory from the repository. That being, my project has the structure:

ProjectDirectory
    src
    war
    etc

I would like the repository to contain src, war, and etc, but not contain the parent directory ProjectDirectory. That's because if I want to clone a copy of the project in my workspace, ProjectDirectory2, the repository for the second project now will try to create a second root directory, ProjectDirectory. Unfortunately, when I try to add a repository for a project using EGit, I seem to only be able to use Team > Share Project on the project folder itself and I don't seem to see anyway to exclude the root directory in the repository from within Eclipse.

Any suggestions on how to skip the top directory in the repository using EGit? I'd prefer being able to do everything from within Eclipse, but if there isn't a way, is there a way to setup the repository this way outside of git, then still be able to use the git control regularly from within git on the repository skipping the top level directory? Thank you much.

Solution

You should commit the project root for multiple reasons:

If you commit only sub directories of your project, you will miss files and folders which are hidden below the project root (e.g. the .settings directory and others). Those need to be committed also, otherwise your project is going to miss information and may not lead to the same results on another machine.
Your wish of trying to clone the same repository a second time in the same workspace sounds very much like you should re-read about git branches. In git, switching between branches is done after a blinking of the eye, so branches should be used when working on different features, versions or otherwise different editions of your project.
The Eclipse project name and the underlying folder name on disk do not need to be the same (watch out for the checkbox "use default location" when creating a new project). So you can checkout a second clone of the project with a different name.
If you later add more projects to your workspace (e.g. a test project), you cannot easily share them into the same git repository, as the content of those additional projects would mix up with the sub directories of the first project in the repository.