Answer yes in a bash script

Add the following to your ~/.ssh/config file:

Host github.com
    StrictHostKeyChecking no

Anything using the open-ssh client to establish a remote shell (with the git client does) should skip the key checks to github.com.

This is actually a bad idea since any form of skipping the checks (whether you automatically hit yes or skip the check in the first place) creates room for a man in the middle security compromise. A better way would be to retrieve and validate the fingerprint and store it in the known_hosts file before needing to run some script that automatically connects.

yes outputs y. RSA key acceptance needs yes. You could try yes yes | git clone [email protected]:repo/repoo.git so yes outputs yes instead of y.

Running ssh-keyscan -H github.com >> ~/.ssh/known_hosts before cloning will add the key and prevent the prompt from appearing.

Of course this approach is also vulnerable to a MITM attack.