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When trying to push to or fetch from a server using Git over SSH, a password dialog is shown in any case. The SSH user does not have a password on the server, but is authenticated using the private-public-key method. This is used by default for platforms like Gitorious (and if I remember correctly, Github as well). When I am using the command-line on Linux, the push works perfectly without any interaction.
Ngit has no integration with the MacOS keychain or ssh agent so this is why you are prompted again for your ssh passphrase. I just finished implementing initial support for storing usernames/passwords in the MacOS keychain and added support for storing passphrases there. Once this support is in monodevelop master you will be prompted to store the passphrase and thus will never need to enter it again. This will not happen until at least monodevelop 2.8.7 though.
Thanks for reporting this.
Actually, can I double check that you actually have a passphrased ssh key. Is the dialog you are given prompting you for a passphrase or do you end up having to log in with a username and/or password?
I use Ubuntu and my experience is that it will not prompt me for a passphrase for my private key at all.
When I try to do a push with Monodevelop I always get a password box, but the password box that comes up will only accept the account password even if I have openssh configured to log in with my private key.
I have not tried using a key without a passphrase.
This should all work with MonoDevelop 2.8.6 and higher. If you experience any issues with these newer builds, either reopen this bug or file a new one. The next major release of monodevelop (due to happen in the next few weeks) should have even better support for the differing authentication methods.