Clone Magento project into a folder with a fresh Magento installation

I have a GitHub repo with my Magento stuff. But i am using .gitignore for the fresh installation files and the repo contains only my files.
On another computer I have a fresh install and now want to clone my custom files from the repo.

So, I tried:

git clone git:// /opt/lampp/htdocs/Magento

but I get a fatal error:

destination path '/opt/lampp/htdocs/Magento' already exists and is not an empty directory.

If I clone without the second parameter (folder path) then I can clone the repo without errors but then it’s in a new Magento duplicated folder Magento/Magento/app/… which is wrong.

OS: Ubuntu 12.04

IDE: NetBeans 7.2.1

Any ideas?

Git Baby is a git and github fan, let's start git clone.