We make a deploy to client's folder at client's server using Jenkins via VPN of several git repos. I've set the "Check out to a sub-directory option" and "Sparse checkout".
We need to deploy only some files of one common repository (other files are private). But if the .git folder is inside, it is not hard to view other files.
For git it is possible to place .git file into repo folder and specify in this file the place to .git folder, e.g.:
my-repo-folder$ cat .git
gitdir: /home/user1/another-my-repo-folder.git
(see more here about gitdir)
Is it possible to set another place of .git folder for git Jenkins plugin like above?
Upd. Here is the deploy configuration of the described above:

Another suggestion :
gitis not a deployment tool (not a good one anyway).If you need to select some files from your repo, and copy only that to the server, you can :