GIT no such identity: id_rsa: No such file or directory

For 2 years, IdentityFile id_rsa worked for me. Today, it accepts only an absolute path as in IdentityFile ~/.ssh/id_rsa. Weird thing.

debug1: Will attempt key: id_rsa  explicit
...
debug1: Trying private key: id_rsa
no such identity: id_rsa: No such file or directory

You've configured the wrong private key path. Try configure it like this.

Host github.com
IdentityFile ~/.ssh/id_rsa