git: osxkeychain credential helper silently fails to remember username/password

Edit ~/.ssh/config and add UseKeychain yes to every host you want the Keychain to remember the password for.

For example, if you are trying to do this for GitHub:

Host github.com    IdentityFile ~/.ssh/your_github_cert_rsa    UseKeychain yes

If you want to enable it for every host, just add:

Host *    UseKeychain yes

This is a new requirement, added by Apple on macOS Sierra 10.12.2, you can learn more about it running man ssh_config in 10.12.2:

UseKeychain             On macOS, specifies whether the system should search for             passphrases in the user's keychain when attempting to use a par-             ticular key. When the passphrase is provided by the user, this             option also specifies whether the passphrase should be stored             into the keychain once it has been verified to be correct.  The             argument must be ``yes'' or ``no''.  The default is ``no''.

Under Mac OS 10.11, you can check if the keychain is disabled with the variable

KeychainIntegration  Specifies whether to enable Keychain support on Mac OS X.    If Keychain support is enabled, then passwords for identities can be   managed via the Mac OS X Keychain.  The value for this keyword must be ``yes'' or ``no''.  The default is ``yes''.AskPassGUI  Show the system password prompt