Clone the repository with the --bare
flag:
git clone --bare ...
A “bare” repository in Git just contains the version control
information and no working files (no tree) and it doesn’t contain the
special .git sub-directory. Instead, it contains all the contents of
the .git sub-directory directly in the main directory itself.
Read more in the documentation on it, or this helpfull page about setting up server environments using the option.