You can use multiple deploy keys for Github created with ssh-keygen following with these steps.
You have to add to your ~/.ssh/config
Host github_deploy_key_1 Hostname github.com User git IdentityFile ~/.ssh/github_deploy_key_1_rsa Host github_deploy_key_2 Hostname github.com User git IdentityFile ~/.ssh/github_deploy_key_2_rsa
If you haven’t added your github name on git:
git config --global user.name "yourgithubname" git config --global user.email "youremail@example.com"
Then clone your repository specifying your custom host, adapting what github suggest to you on repo page:
git clone git@github_deploy_key_1:yourgithubname/your-repo.git
If you have enabled push permissions you can use this deploy key even to update the repository.
In this way you can keep a server clean from your github passepartout and add only the keys it needs.