Git always prompts "Are you sure you want to continue connecting (yes/no/[fingerprint])?"

Question

I have ssh setup in ~/.config/ssh instead of the default ~/.ssh.

Every time I do a git pull or git push, I get the below message:

The authenticity of host 'github.com (192.30.255.112)' can't be established.
RSA key fingerprint is SHA256:....
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
Failed to add the host to the list of known hosts (/Users/username/.ssh/known_hosts).

After entering yes, the next step of adding the host to the known_hosts fails, but the operation (git pull and git push) completes successfully.

There is no ~/.ssh (and thereby no ~/.ssh/known_hosts) after the operation completes.

The location of my known hosts file is: ~/.config/ssh/known_hosts.

I have already done:

ssh -o UserKnownHostsFile=~/.config/ssh/known_hosts -T [email protected]

and

eval $(ssh-agent)
ssh-add -K ~/.config/ssh/id_rsa

and also added the SSH keys to my github profile using pbcopy < ~/.config/ssh/id_rsa.pub.

Contents of ~/.config/ssh/config:

Host *
  AddKeysToAgent yes
  UseKeychain yes
  IdentityFile ~/.config/ssh/id_rsa

Contents of ~/.config/ssh/known_hosts:

github.com,192.30.255.112 ssh-rsa ...
...
...==
192.30.255.113 ssh-rsa ...
...
...==

File permissions of ~/.config/ssh:

drwxr-xr-x  6 username  staff   192 Aug 29 19:12 .
drwxr-xr-x  7 username  staff   224 Aug 29 16:17 ..
-rw-r--r--  1 username  staff    83 Aug 29 19:01 config
-rw-------  1 username  staff  3434 Aug 29 19:00 id_rsa
-rw-r--r--  1 username  staff   747 Aug 29 19:00 id_rsa.pub
-rw-r--r--  1 username  staff   803 Aug 29 19:31 known_hosts

EDIT:

Doing ssh -o UserKnownHostsFile=$HOME/.config/ssh/known_hosts [email protected] gives:

[email protected]: Permission denied (publickey)

How do I avoid entering 'yes' at every git pull and git push ?

Solution

Following the instructions on this GitHub page, I executed the command ssh -vT [email protected].

It gave the below output:

OpenSSH_8.1p1, LibreSSL 2.7.3
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 47: Applying options for *
debug1: Connecting to github.com port 22.
debug1: Connection established.
debug1: identity file /Users/saurabh/.ssh/id_rsa type -1
debug1: identity file /Users/saurabh/.ssh/id_rsa-cert type -1
debug1: identity file /Users/saurabh/.ssh/id_dsa type -1
debug1: identity file /Users/saurabh/.ssh/id_dsa-cert type -1
debug1: identity file /Users/saurabh/.ssh/id_ecdsa type -1
debug1: identity file /Users/saurabh/.ssh/id_ecdsa-cert type -1
debug1: identity file /Users/saurabh/.ssh/id_ed25519 type -1
debug1: identity file /Users/saurabh/.ssh/id_ed25519-cert type -1
debug1: identity file /Users/saurabh/.ssh/id_xmss type -1
debug1: identity file /Users/saurabh/.ssh/id_xmss-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_8.1
debug1: Remote protocol version 2.0, remote software version babeld-c2ee9279
debug1: no match: babeld-c2ee9279
debug1: Authenticating to github.com:22 as 'git'
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: algorithm: curve25519-sha256
debug1: kex: host key algorithm: rsa-sha2-512
debug1: kex: server->client cipher: [email protected] MAC: <implicit> compression: none
debug1: kex: client->server cipher: [email protected] MAC: <implicit> compression: none
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: Server host key: ssh-rsa SHA256:...
debug1: Host 'github.com' is known and matches the RSA host key.
debug1: Found key in /Users/saurabh/.ssh/known_hosts:1
debug1: rekey out after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: rekey in after 134217728 blocks
debug1: Will attempt key: [email protected] RSA SHA256:...
debug1: Will attempt key: /Users/saurabh/.ssh/id_rsa 
debug1: Will attempt key: /Users/saurabh/.ssh/id_dsa 
debug1: Will attempt key: /Users/saurabh/.ssh/id_ecdsa 
debug1: Will attempt key: /Users/saurabh/.ssh/id_ed25519 
debug1: Will attempt key: /Users/saurabh/.ssh/id_xmss 
debug1: SSH2_MSG_EXT_INFO received
debug1: kex_input_ext_info: server-sig-algs=<ssh-ed25519,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,ssh-rsa,rsa-sha2-512,rsa-sha2-256,ssh-dss>
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Offering public key: [email protected] RSA SHA256:...
debug1: Authentications that can continue: publickey
debug1: Trying private key: /Users/saurabh/.ssh/id_rsa
debug1: Trying private key: /Users/saurabh/.ssh/id_dsa
debug1: Trying private key: /Users/saurabh/.ssh/id_ecdsa
debug1: Trying private key: /Users/saurabh/.ssh/id_ed25519
debug1: Trying private key: /Users/saurabh/.ssh/id_xmss
debug1: No more authentication methods to try.
[email protected]: Permission denied (publickey).

And the "-1" at the end of the "identity file" lines means SSH couldn't find a file to use.

I modified this answer so that the private key is configured globally, to:

git config --global core.sshCommand "ssh -i $HOME/.config/ssh/id_rsa -F /dev/null"